iqtree: iqtree.xml annotate

annotate iqtree.xml @ 11:563c3aa769f2 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f"

author	iuc
date	Mon, 27 Sep 2021 15:55:35 +0000
parents	b8476e82ac20
children	9b892d7f82cc

rev	line source
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	1 <tool id="iqtree" name="IQ-TREE" version="@TOOL_VERSION@+@VERSION_SUFFIX@" >
0 05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	2 <description>Phylogenomic / evolutionary tree construction from multiple sequences</description>
2 d1c340a5664b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 686710a7d313b828f1daed20c4055479727f2d91 iuc parents: 1 diff changeset	3 <macros>
11 563c3aa769f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f" iuc parents: 10 diff changeset	4 <token name="@VERSION_SUFFIX@">galaxy2</token>
2 d1c340a5664b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 686710a7d313b828f1daed20c4055479727f2d91 iuc parents: 1 diff changeset	5 <import>iqtree_macros.xml</import>
d1c340a5664b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 686710a7d313b828f1daed20c4055479727f2d91 iuc parents: 1 diff changeset	6 </macros>
d1c340a5664b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 686710a7d313b828f1daed20c4055479727f2d91 iuc parents: 1 diff changeset	7 <expand macro="requirements" />
4 f97743d52b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386" iuc parents: 3 diff changeset	8 <command detect_errors="exit_code"><![CDATA[
0 05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	9 iqtree
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	10 --prefix PREF
4 f97743d52b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386" iuc parents: 3 diff changeset	11 #if $general_options.short_alignments:
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	12 -T 1
4 f97743d52b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386" iuc parents: 3 diff changeset	13 #else:
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	14 -T \${GALAXY_SLOTS:-10}
4 f97743d52b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386" iuc parents: 3 diff changeset	15 #end if
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	16 --redo
0 05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	17
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	18 ## file
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	19 #if $general_options.s
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	20 -s '$general_options.s'
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	21 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	22
7 524d31add34a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af" iuc parents: 6 diff changeset	23 #if $general_options.o
524d31add34a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af" iuc parents: 6 diff changeset	24 -o '$general_options.o'
524d31add34a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af" iuc parents: 6 diff changeset	25 #end if
524d31add34a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af" iuc parents: 6 diff changeset	26
0 05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	27 ## file
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	28 #if $general_options.t
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	29 -t '$general_options.t'
11 563c3aa769f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f" iuc parents: 10 diff changeset	30 $tree_parameters.constructing_consensus.contree
563c3aa769f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f" iuc parents: 10 diff changeset	31 $tree_parameters.constructing_consensus.connet
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	32 #if str($tree_parameters.constructing_consensus.burnin) != ''
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	33 --burnin '$tree_parameters.constructing_consensus.burnin'
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	34 #end if
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	35
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	36 ## file
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	37 #if $tree_parameters.constructing_consensus.support
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	38 --support '$tree_parameters.constructing_consensus.support'
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	39 #end if
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	40
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	41 #if str($tree_parameters.constructing_consensus.suptag) != ''
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	42 --suptag '$tree_parameters.constructing_consensus.suptag'
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	43 #end if
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	44
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	45 ## file
11 563c3aa769f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f" iuc parents: 10 diff changeset	46 #if $tree_parameters.computing_robinson_foulds.tree_dist_all
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	47 $tree_parameters.computing_robinson_foulds.tree_dist_all
11 563c3aa769f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f" iuc parents: 10 diff changeset	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" iuc parents: 10 diff changeset	49 --tree-dist2 $tree_parameters.computing_robinson_foulds.tree_dist2
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	50 #end if
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	51 $tree_parameters.ancestral_state.ancestral
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	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" iuc parents: 4 diff changeset	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" iuc parents: 4 diff changeset	54 #end if
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	55 #if $tree_parameters.concordance_factor.gcf:
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	56 --gcf '$tree_parameters.concordance_factor.gcf'
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	57 #end if
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	58 #if $tree_parameters.concordance_factor.scf:
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	59 --scf '$tree_parameters.concordance_factor.scf'
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	60 #end if
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	61 $tree_parameters.concordance_factor.df_tree
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	62 $tree_parameters.concordance_factor.cf_verbose
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	63 $tree_parameters.concordance_factor.cf_quartet
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	64 $tree_parameters.symmetry_test.symtest
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	65 $tree_parameters.symmetry_test.symtest_remove_bad
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	66 $tree_parameters.symmetry_test.symtest_remove_good
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	67 $tree_parameters.symmetry_test.symtest_keep_zero
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	68 #if $tree_parameters.symmetry_test.symtest_pval:
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	69 --symtest-pval $tree_parameters.symmetry_test.symtest_pval
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	70 #end if
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	71 #if $tree_parameters.symmetry_test.symtest_type:
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	72 --symtest-type $tree_parameters.symmetry_test.symtest_type
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	73 #end if
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	74 #end if
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	75
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	76 ## date options
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	77 #if str($time_tree.date_source.select_source) == 'dataset':
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	78 #if $time_tree.date_source.date:
8 c1d53e95327f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit a58c8d3c985688e49908dfeceab5be4352d71563" iuc parents: 7 diff changeset	79 --date '$time_tree.date_source.date'
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	80 #end if
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	81 #elif str($time_tree.date_source.select_source) == 'input':
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	82 --date TAXNAME
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	83 #if str($time_tree.date_source.date_tip) != '':
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	84 --date-tip '$time_tree.date_source.date_tip'
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	85 #end if
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	86 #if str($time_tree.date_source.date_root) != '':
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	87 --date-root '$time_tree.date_source.date_root'
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	88 #end if
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	89 #if str($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 parents: 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 $general_options.safe
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	116
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	117 #if str($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 parents: 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 parents: 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 parents: 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 $modelling_parameters.automatic_model.cond_model.opt_custommodel:
0 05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	129 -m '$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 '$modelling_parameters.automatic_model.cond_model.m'
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	136 #end if
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	137 #end if
0 05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	138 #end if
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	139
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	140 #if str($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 $modelling_parameters.automatic_model.merge_strategy.rcluster_max
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	150 #end if
0 05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	151 #end if
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	152
0 05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	153 #if str($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 '$modelling_parameters.automatic_model.mset'
0 05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	155 #end if
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	156
0 05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	157 #if str($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 iuc parents: diff changeset	366 </command>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	367 <inputs>
4 f97743d52b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386" iuc parents: 3 diff changeset	368 <section name="general_options" expanded="true" title="General options">
8 c1d53e95327f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit a58c8d3c985688e49908dfeceab5be4352d71563" iuc parents: 7 diff changeset	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."/>
7 524d31add34a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af" iuc parents: 6 diff changeset	370 <param argument="-o" type="text" optional="true" label="Comma-separated list of taxons to output">
524d31add34a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af" iuc parents: 6 diff changeset	371 <expand macro="sanitize_query" />
524d31add34a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af" iuc parents: 6 diff changeset	372 </param>
524d31add34a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af" iuc parents: 6 diff changeset	373
524d31add34a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af" iuc parents: 6 diff changeset	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." />
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	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">
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	376 <help><![CDATA[
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	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.
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	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).]]>
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	379 </help>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	380 <option value="DNA">DNA</option>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	381 <option value="AA">AA</option>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	382 <option value="BIN">BIN</option>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	383 <option value="MORPH">MORPH</option>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	384 <option value="CODON">CODON</option>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	385 <option value="NT2AA">NT2AA</option>
0 05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	386 </param>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	387 <param argument="-t" type="data" format="nhx" optional="true" label="Specify a file containing starting tree for tree search"/>
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	388 <param argument="--seed" type="integer" optional="true" label="Specify a random number seed to reproduce a previous run (leave blank to randomize)"/>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	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."/>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	390 <param argument="--epsilon" type="float" optional="true" min="0" max="1" label="Likelihood epsilon for parameter estimate" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	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."/>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	392 </section>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	393 <section name="time_tree" expanded="false" title="Time Tree Reconstruction">
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	394 <conditional name="date_source">
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	395 <param name="select_source" type="select" label="Source of date information">
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	396 <option value="none">Skip time tree reconstruction</option>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	397 <option value="dataset">Text file</option>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	398 <option value="input">Derive from input</option>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	399 </param>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	400 <when value="none" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	401 <when value="input" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	402 <when value="dataset">
8 c1d53e95327f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit a58c8d3c985688e49908dfeceab5be4352d71563" iuc parents: 7 diff changeset	403 <param argument="--date" type="data" format="txt,tabular" optional="true" label="File containing dates of tips or ancestral nodes" />
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	404 </when>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	405 </conditional>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	406 <param argument="--date-tip" type="text" optional="true" label="Tip dates as a real number or YYYY-MM-DD">
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	407 <expand macro="sanitize_query" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	408 </param>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	409 <param argument="--date-root" type="text" optional="true" label="Root date as a real number or YYYY-MM-DD">
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	410 <expand macro="sanitize_query" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	411 </param>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	412 <param argument="--date-ci" type="integer" optional="true" label="Number of replicates to compute confidence interval" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	413 <param argument="--clock-sd" type="float" optional="true" label="Standard-deviation for lognormal relaxed clock" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	414 <param argument="--date-no-outgroup" type="boolean" truevalue="--date-no-outgroup" falsevalue="" label="Exclude outgroup from time tree" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	415 <param argument="--date-outlier" type="integer" optional="true" label="Z-score cutoff to remove outlier tips/nodes" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	416 <param argument="--date-options" type="text" optional="true" label="Extra options passing directly to LSD2">
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	417 <expand macro="sanitize_query" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	418 </param>
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	419 </section>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	420 <section name="likelihood_mapping" expanded="False" title="Likelihood mapping analysis">
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	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."/>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	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."/>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	423 <param argument="--quartetlh" type="boolean" truevalue="--quartetlh" falsevalue="" checked="false" label="Write quartet log-likelihoods into .lmap.quartetlh file (typically not needed)."/>
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	424 </section>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	425 <section name="modelling_parameters" title="Modelling Parameters">
0 05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	426 <section name="automatic_model" expanded="False" title="Automatic model selection">
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	427 <conditional name="cond_model" >
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	428 <param name="opt_custommodel" type="boolean" checked="false" label="Use Custom Model" help="See http://www.iqtree.org/doc/Substitution-Models"/>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	429 <when value="true">
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	430 <param argument="-m" type="text" label="Model">
3 973a28be3b7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 73ef23e40772952e5fde0576d66fa81de4916058" iuc parents: 2 diff changeset	431 <expand macro="sanitize_query"
973a28be3b7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 73ef23e40772952e5fde0576d66fa81de4916058" iuc parents: 2 diff changeset	432 validinitial="string.ascii_uppercase,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	433 </param>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	434 </when>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	435 <when value="false">
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	436 <param argument="-m" type="select" label="Perform standard model selection like jModelTest (for DNA) and ProtTest (for protein)" >
6 224c75ad0518 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01" iuc parents: 5 diff changeset	437 <help><![CDATA[
224c75ad0518 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01" iuc parents: 5 diff changeset	438 <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/>
224c75ad0518 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01" iuc parents: 5 diff changeset	439 IQ-TREE also works for codon, binary and morphogical data.
224c75ad0518 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01" iuc parents: 5 diff changeset	440 <table>
224c75ad0518 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01" iuc parents: 5 diff changeset	441 <tr>
224c75ad0518 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01" iuc parents: 5 diff changeset	442 <td><i>TESTONLY</i></td>
224c75ad0518 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01" iuc parents: 5 diff changeset	443 <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>
224c75ad0518 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01" iuc parents: 5 diff changeset	444 </tr>
224c75ad0518 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01" iuc parents: 5 diff changeset	445 <tr>
224c75ad0518 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01" iuc parents: 5 diff changeset	446 <td><i>TEST</i></td>
224c75ad0518 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01" iuc parents: 5 diff changeset	447 <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>
224c75ad0518 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01" iuc parents: 5 diff changeset	448 </tr>
224c75ad0518 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01" iuc parents: 5 diff changeset	449 <tr>
224c75ad0518 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01" iuc parents: 5 diff changeset	450 <td><i>MF</i></td>
224c75ad0518 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01" iuc parents: 5 diff changeset	451 <td>Best-fit model selection without tree reconstruction.</td>
224c75ad0518 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01" iuc parents: 5 diff changeset	452 </tr>
224c75ad0518 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01" iuc parents: 5 diff changeset	453 <tr>
224c75ad0518 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01" iuc parents: 5 diff changeset	454 <td><i>MFP</i></td>
224c75ad0518 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01" iuc parents: 5 diff changeset	455 <td>Extended model selection with FreeRate heterogeneity immediately followed by tree inference.</td>
224c75ad0518 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01" iuc parents: 5 diff changeset	456 </tr>
224c75ad0518 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01" iuc parents: 5 diff changeset	457 </table>
224c75ad0518 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01" iuc parents: 5 diff changeset	458 ]]>
224c75ad0518 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01" iuc parents: 5 diff changeset	459 </help>
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	460 <option value="" selected="true">(None)</option>
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	461 <option value="TESTONLY">Standard model selection</option>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	462 <option value="TEST">Standard model selection followed by tree inference</option>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	463 <option value="MF">Extended model selection with FreeRate heterogeneity</option>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	464 <option value="MFP">Extended model selection followed by tree inference</option>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	465 </param>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	466 <param name="additional_models" type="text" optional="true" label="Additional model specifications" help="See http://www.iqtree.org/doc/Substitution-Models">
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	467 <expand macro="sanitize_query" />
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	468 </param>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	469 </when>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	470 </conditional>
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	471 <conditional name="merge_strategy">
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	472 <param argument="--merge" type="select" label="Merge partitions">
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	473 <option value="none">Do not merge</option>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	474 <option value="rclusterf">Merge using rcluster relaxed algorithm</option>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	475 <option value="rcluster">Merge using rcluster algorithm</option>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	476 <option value="greedy">Merge using greedy algorithm</option>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	477 </param>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	478 <when value="none" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	479 <when value="greedy" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	480 <when value="rcluster">
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	481 <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." />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	482 <param argument="--rcluster-max" type="integer" optional="true" label="Max number of partition pairs" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	483 </when>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	484 <when value="rclusterf">
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	485 <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." />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	486 <param argument="--rcluster-max" type="integer" optional="true" label="Max number of partition pairs" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	487 </when>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	488 </conditional>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	489 <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.">
2 d1c340a5664b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 686710a7d313b828f1daed20c4055479727f2d91 iuc parents: 1 diff changeset	490 <expand macro="sanitize_query"
10 b8476e82ac20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1bda7ff567a523740d76eea8d7df6db97c905693" iuc parents: 9 diff changeset	491 validinitial="string.ascii_letters,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	492 </param>
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	493 <param argument="--msub" type="select" label="Specify either nuclear, mitochondrial, chloroplast or viral to restrict to those AA models designed for specified source." help="">
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	494 <option value="nuclear">nuclear</option>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	495 <option value="mitochondrial">mitochondrial</option>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	496 <option value="chloroplast">chloroplast</option>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	497 <option value="viral">viral</option>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	498 </param>
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	499 <param argument="--mfreq" type="text" optional="true" label="Specify a comma-separated list of frequency types for model selection" >
2 d1c340a5664b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 686710a7d313b828f1daed20c4055479727f2d91 iuc parents: 1 diff changeset	500 <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	501 validinitial="string.ascii_uppercase,string.digits,x,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	502 </param>
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	503 <param argument="--mrate" type="text" optional="true" label="Specify a comma-separated list of rate heterogeneity types for model selection">
2 d1c340a5664b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 686710a7d313b828f1daed20c4055479727f2d91 iuc parents: 1 diff changeset	504 <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	505 validinitial="string.ascii_uppercase,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	506 </param>
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	507 <param argument="--cmin" type="integer" value="2" optional="true" label="Specify minimum number of categories for FreeRate model"/>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	508 <param argument="--cmax" type="integer" value="10" optional="true" label="Specify maximum number of categories for FreeRate model"/>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	509 <param argument="--merit" type="select" label="Specify either AIC, AICc or BIC for the optimality criterion to apply for new procedure" help="">
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	510 <option value="AIC">AIC</option>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	511 <option value="AICc">AICc</option>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	512 <option value="BIC">BIC</option>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	513 </param>
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	514 <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"/>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	515 <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.">
2 d1c340a5664b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 686710a7d313b828f1daed20c4055479727f2d91 iuc parents: 1 diff changeset	516 <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	517 validinitial="string.ascii_uppercase,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	518 </param>
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	519 <param argument="--mdef" type="data" format="txt" optional="true" label="Specify a NEXUS model file to define new models."/>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	520 <param argument="--modelomatic" type="boolean" truevalue="--modelomatic" falsevalue="" label="Find best codon/protein/DNA models" />
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	521 </section>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	522 <section name="specifying_substitution" expanded="False" title="Specifying substitution models">
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	523 <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."/>
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	524 </section>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	525 <section name="rate_heterogeneity" expanded="False" title="Rate heterogeneity">
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	526 <param argument="--alpha-min" type="text" optional="true" label="Specify the minimum Gamma shape parameter (default: estimate)">
2 d1c340a5664b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 686710a7d313b828f1daed20c4055479727f2d91 iuc parents: 1 diff changeset	527 <expand macro="sanitize_query" />
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	528 </param>
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	529 <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)"/>
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	530 <param argument="-i" type="text" optional="true" label="Specify the proportion of invariable sites (default: estimate)">
2 d1c340a5664b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 686710a7d313b828f1daed20c4055479727f2d91 iuc parents: 1 diff changeset	531 <expand macro="sanitize_query" />
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	532 </param>
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	533 <param argument="--opt-gamma-inv" type="boolean" truevalue="--opt-gamma-inv" falsevalue="" checked="false" label="Perform more thorough estimation for +I+G model parameters"/>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	534 <param argument="--rate" type="boolean" truevalue="--rate" falsevalue="" checked="false" label="Write empirical Bayesian site rates to .rate file"/>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	535 <param argument="--mlrate" type="boolean" truevalue="--mlrate" falsevalue="" checked="false" label="Write maximum likelihood site rates to .mlrate file"/>
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	536 </section>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	537 <section name="partition_model" expanded="False" title="Partition model options">
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	538 <conditional name="model_selection">
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	539 <param name="model" type="select" label="Partition model">
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	540 <option value="none">No partition model</option>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	541 <option value="p">Edge-linked proportional partition model</option>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	542 <option value="q">Edge-linked equal partition model</option>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	543 <option value="Q">Edge-unlinked proportional partition model</option>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	544 <option value="S">Separate tree inference</option>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	545 </param>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	546 <when value="none" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	547 <when value="p">
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	548 <param argument="-p" type="data" format="nex" optional="true" label="Partition file" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	549 <param argument="--subsample" type="integer" optional="true" label="Subsample partitions" help="Use a negative value for complement" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	550 <param argument="--subsample-seed" type="integer" optional="true" label="Subsampling random seed" help="Use a negative value for complement" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	551 </when>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	552 <when value="q">
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	553 <param argument="-q" type="data" format="nex" optional="true" label="Partition file" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	554 <param argument="--subsample" type="integer" optional="true" label="Subsample partitions" help="Use a negative value for complement" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	555 <param argument="--subsample-seed" type="integer" optional="true" label="Subsampling random seed" help="Use a negative value for complement" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	556 </when>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	557 <when value="Q">
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	558 <param argument="-Q" type="data" format="nex" optional="true" label="Partition file" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	559 <param argument="--subsample" type="integer" optional="true" label="Subsample partitions" help="Use a negative value for complement" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	560 <param argument="--subsample-seed" type="integer" optional="true" label="Subsampling random seed" help="Use a negative value for complement" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	561 </when>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	562 <when value="S">
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	563 <param argument="-S" type="data" format="nex" optional="true" label="Partition file" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	564 <param argument="--subsample" type="integer" optional="true" label="Subsample partitions" help="Use a negative value for complement" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	565 <param argument="--subsample-seed" type="integer" optional="true" label="Subsampling random seed" help="Use a negative value for complement" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	566 </when>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	567 </conditional>
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	568 </section>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	569 <section name="site_specific_frequency" expanded="False" title="Site-specific frequency model options">
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	570 <param argument="--tree-freq" type="data" format="nhx" optional="true" label="Specify a guide tree to infer site frequency profiles."/>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	571 <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."/>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	572 <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."/>
0 05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	573 </section>
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	574 </section>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	575 <section name="tree_parameters" title="Tree Parameters">
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	576 <section name="tree_search" expanded="False" title="Tree search parameters">
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	577 <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)." />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	578 <param argument="--ninit" type="integer" value="100" optional="true" label="Specify number of initial parsimony trees"/>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	579 <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"/>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	580 <param argument="--nbest" type="integer" value="5" optional="true" label="Specify number of trees in the candidate set to maintain during ML tree search"/>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	581 <param argument="--nstop" type="integer" value="100" optional="true" label="Specify number of unsuccessful iterations to stop"/>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	582 <param argument="--radius" type="integer" value="6" optional="true" label="Specify SPR radius for the initial parsimony tree search"/>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	583 <param argument="--perturb" type="float" value="0.5" optional="true" label="Specify perturbation strength (between 0 and 1) for randomized NNI"/>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	584 <param argument="--allnni" type="boolean" truevalue="-allnni" falsevalue="" checked="false" label="Turn on more thorough and slower NNI search"/>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	585 <param argument="--tree-fix" type="boolean" truevalue="--tree-fix" falsevalue="" checked="false" label="Avoid computing ML pairwise distances and BIONJ tree."/>
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	586 <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."/>
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	587 <param argument="--fast" type="boolean" truevalue="--fast" falsevalue="" label="Fast search to resemble FastTree" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	588 <param argument="--polytomy" type="boolean" truevalue="--polytomy" falsevalue="" label="Collapse near-zero branches into polytomy" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	589 <param argument="--treels" type="boolean" truevalue="--treels" falsevalue="" label="Write locally optimal trees into .treels file" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	590 <param argument="--show-lh" type="boolean" truevalue="--show-lh" falsevalue="" label="Compute tree likelihood without optimisation" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	591 <param argument="--terrace" type="boolean" truevalue="--terrace" falsevalue="" label="Check if the tree lies on a phylogenetic terrace" />
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	592 </section>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	593 <section name="single_branch" expanded="False" title="Single branch tests">
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	594 <param argument="--alrt" type="integer" optional="true" label="Specify number of replicates (>=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."/>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	595 <param argument="--abayes" type="boolean" truevalue="-abayes" falsevalue="" checked="false" label="Perform approximate Bayes test (Anisimova et al., 2011)."/>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	596 <param argument="--lbp" type="integer" optional="true" label="Specify number of replicates (>=1000) to perform fast local bootstrap probability method (Adachi and Hasegawa, 1996)."/>
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	597 </section>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	598 <section name="tree_topology" expanded="False" title="Tree topology tests">
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	599 <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."/>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	600 <param argument="--test" type="integer" optional="true" label="Specify the number of RELL (Kishino et al., 1990) replicates (>=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)."/>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	601 <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."/>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	602 <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."/>
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	603 </section>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	604 <section name="constructing_consensus" expanded="False" title="Constructing consensus tree">
11 563c3aa769f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f" iuc parents: 10 diff changeset	605 <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."/>
563c3aa769f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f" iuc parents: 10 diff changeset	606 <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."/>
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	607 <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"/>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	608 <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."/>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	609 <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."/>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	610 <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."/>
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	611 </section>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	612 <section name="computing_robinson_foulds" expanded="False" title="Computing Robinson-Foulds distance">
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	613 <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"/>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	614 <param argument="--tree-dist" type="data" format="nhx" optional="true" label="Compute RF distances between -t trees and this set" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	615 <param argument="--tree-dist2" type="data" format="nhx" optional="true" label="Like -rf but trees can have unequal taxon sets" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	616
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	617 </section>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	618 <section name="generating_random" expanded="False" title="Generating random trees">
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	619 <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"/>
6 224c75ad0518 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01" iuc parents: 5 diff changeset	620 <param argument="--rand" type="select" optional="true" label="Random tree creation">
224c75ad0518 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01" iuc parents: 5 diff changeset	621 <option value="--rand UNI">Uniform model</option>
224c75ad0518 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01" iuc parents: 5 diff changeset	622 <option value="--rand CAT">Random caterpillar tree</option>
224c75ad0518 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01" iuc parents: 5 diff changeset	623 <option value="--rand BAL">Random balanced tree</option>
224c75ad0518 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01" iuc parents: 5 diff changeset	624 </param>
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	625 <param name="branch_min" type="integer" optional="true" label="Minimum branch lengths of the random tree" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	626 <param name="branch_mean" type="integer" optional="true" label="Median branch lengths of the random tree" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	627 <param name="branch_max" type="integer" optional="true" label="Maximum branch lengths of the random tree" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	628 </section>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	629 <section name="ancestral_state" title="Ancestral State Reconstruction">
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	630 <param argument="--ancestral" type="boolean" truevalue="--ancestral" falsevalue="" label="Perform ancestral state reconstruction by empirical Bayes" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	631 <param argument="--asr-min" type="float" optional="true" min="0" max="1" label="Minimum probability of ancestral state" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	632 </section>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	633 <section name="symmetry_test" title="Symmetry Tests">
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	634 <param argument="--symtest" type="boolean" truevalue="--symtest" falsevalue="" label="Perform three tests of symmetry" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	635 <param argument="--symtest-remove-bad" type="boolean" truevalue="--symtest-remove-bad" falsevalue="" label="Do --symtest and remove bad partitions" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	636 <param argument="--symtest-remove-good" type="boolean" truevalue="--symtest-remove-good" falsevalue="" label="Do --symtest and remove good partitions" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	637 <param argument="--symtest-type" type="select" optional="true" label="Type of test to use">
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	638 <option value="MAR">Marginal</option>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	639 <option value="INT">Internal</option>
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	640 </param>
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	641 <param argument="--symtest-pval" type="float" optional="true" label="P-value cutoff" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	642 <param argument="--symtest-keep-zero" type="boolean" truevalue="--symtest-keep-zero" falsevalue="" label="Keep NAs in the tests" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	643 </section>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	644 <section name="concordance_factor" title="Concordance Factor Analysis">
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	645 <param argument="--gcf" type="data" format="nex" optional="true" label="Set of source trees for gene concordance factor" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	646 <param argument="--df-tree" type="boolean" truevalue="--df-tree" falsevalue="" label="Write discordant trees associated with gDF1" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	647 <param argument="--scf" type="integer" optional="true" label="Number of quartets for site concordance factor" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	648 <param argument="--cf-verbose" type="boolean" truevalue="--cf-verbose" falsevalue="" label="Write CF per tree/locus" />
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	649 <param argument="--cf-quartet" type="boolean" truevalue="--cf-quartet" falsevalue="" label="Write sCF for all resampled quartets to .cf.quartet" />
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	650 </section>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	651 </section>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	652 <section name="bootstrap_parameters" title="Bootstrap Parameters">
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	653 <section name="ultrafast_bootstrap" expanded="False" title="Ultrafast bootstrap parameters">
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	654 <param argument="--ufboot" type="integer" optional="true" label="Specify number of bootstrap replicates (>=1000)."/>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	655 <param argument="--ufjack" type="integer" optional="true" label="Specify number of replicates for ultrafast jackknife (>=1000)."/>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	656 <param argument="--jack-prop" type="float" optional="true" min="0" max="1" label="Subsampling proportion for jackknife." help="Default: 0.5"/>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	657 <param argument="--boot-trees" type="boolean" truevalue="--boot-trees" falsevalue="" checked="false" label="Turn on writing bootstrap trees to .ufboot file"/>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	658 <param argument="--wbtl" type="boolean" truevalue="--wbtl" falsevalue="" checked="false" label="Like -boot-trees but bootstrap trees written with branch lengths"/>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	659 <param argument="--nmax" type="integer" value="1000" optional="true" label="Specify maximum number of iterations to stop"/>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	660 <param argument="--bcor" type="float" value="0.99" optional="true" label="Specify minimum correlation coefficient for UFBoot convergence criterion"/>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	661 <param argument="--nstep" type="integer" value="100" optional="true" label="Specify iteration interval checking for UFBoot convergence"/>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	662 <param argument="--beps" type="float" value="0.5" optional="true" label="Specify a small epsilon to break tie in RELL evaluation for bootstrap trees"/>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	663 <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).">
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	664 <sanitizer>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	665 <valid initial="string.ascii_uppercase" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	666 </sanitizer>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	667 </param>
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	668 <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."/>
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	669 </section>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	670 <section name="nonparametric_bootstrap" expanded="False" title="Nonparametric bootstrap">
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	671 <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."/>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	672 <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."/>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	673 <param argument="--jack-prop" type="float" optional="true" min="0" max="1" label="Subsampling proportion for jackknife." help="Default: 0.5"/>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	674 <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	675 <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	676 <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	677 </section>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	678 </section>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	679 <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	680 <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	681 <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	682 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	683 </param>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	684 </section>
0 05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	685 </inputs>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	686 <outputs>
4 f97743d52b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386" iuc parents: 3 diff changeset	687 <data name="bionj" format="nhx" from_work_dir="*.bionj" label="${tool.name} on ${on_string}: BIONJ Tree" />
f97743d52b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386" iuc parents: 3 diff changeset	688 <data name="treefile" format="nhx" from_work_dir="*.treefile" label="${tool.name} on ${on_string}: MaxLikelihood Tree" />
11 563c3aa769f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f" iuc parents: 10 diff changeset	689 <data name="consensus_tree" format="nhx" from_work_dir="*.contree" label="${tool.name} on ${on_string}: Consensus Tree">
563c3aa769f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f" iuc parents: 10 diff changeset	690 <filter>tree_parameters['constructing_consensus']['contree']</filter>
563c3aa769f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f" iuc parents: 10 diff changeset	691 </data>
4 f97743d52b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386" iuc parents: 3 diff changeset	692 <data name="mldist" format="mldist" from_work_dir="*.mldist" label="${tool.name} on ${on_string}: MaxLikelihood Distance Matrix"/>
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	693 <data name="splits" format="nex" from_work_dir="*.splits.nex" label="${tool.name} on ${on_string}: Occurence Frequencies in Bootstrap Trees" />
4 f97743d52b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386" iuc parents: 3 diff changeset	694 <data name="iqtree" format="iqtree" from_work_dir="*.iqtree" label="${tool.name} on ${on_string}: Report and Final Tree" />
7 524d31add34a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af" iuc parents: 6 diff changeset	695 <data name="mlrate" format="data" from_work_dir="*.mlrate" label="${tool.name} on ${on_string}: ML Rates">
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	696 <filter>modelling_parameters['rate_heterogeneity']['mlrate']</filter>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	697 </data>
7 524d31add34a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af" iuc parents: 6 diff changeset	698 <data name="timetree" format="nex" from_work_dir="PREF.timetree.nex" label="${tool.name} on ${on_string}: Tree labeled with dates">
524d31add34a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af" iuc parents: 6 diff changeset	699 <filter>time_tree['date_source']['select_source'] != 'none'</filter>
524d31add34a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af" iuc parents: 6 diff changeset	700 </data>
9 f58a10e2e46d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 00ddca12cd441fab5c928f93c62fa8aa79160967" iuc parents: 8 diff changeset	701 <data name="lsd_report" format="txt" from_work_dir="PREF.timetree.lsd" label="${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	702 <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	703 </data>
0 05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	704 </outputs>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	705 <tests>
11 563c3aa769f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f" iuc parents: 10 diff changeset	706 <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	707 <param name="seed" value="1257" />
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	708 <param name="seqtype" value="AA" />
0 05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	709 <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	710 <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	711 <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	712 <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	713 <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	714 <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	715 <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	716 <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	717 <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	718 <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	719 </assert_contents>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	720 </output>
4 f97743d52b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386" iuc parents: 3 diff changeset	721 <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	722 <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	723 <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	724 </assert_contents>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	725 </output>
4 f97743d52b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386" iuc parents: 3 diff changeset	726 <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	727 <assert_contents>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	728 <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	729 <has_line_matching expression="^Whale(\s+((\d\|\.)+))+\s+$" />
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	730 <has_line_matching expression="^Cow(\s+((\d\|\.)+))+\s+$" />
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	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 </output>
4 f97743d52b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386" iuc parents: 3 diff changeset	733 <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	734 <assert_contents>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	735 <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	736 </assert_contents>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	737 </output>
11 563c3aa769f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f" iuc parents: 10 diff changeset	738 <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	739 <assert_contents>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	740 <has_line_matching
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	741 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	742 </assert_contents>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	743 </output>
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	744 <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	745 <assert_contents>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	746 <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	747 <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	748 </assert_contents>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	749 </output>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	750 </test>
11 563c3aa769f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f" iuc parents: 10 diff changeset	751 <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	752 <!-- 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	753 <param name="seed" value="1257" />
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	754 <param name="seqtype" value="AA" />
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	755 <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	756 <!-- <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	757 <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	758 <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	759 <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	760 <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	761 <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	762 <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	763 <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	764 <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	765 <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	766 <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	767 <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	768 <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	769 <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	770 <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	771 <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	772 <param name="beps" value="0.5" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	773 <param name="b" value="2" />
4 f97743d52b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386" iuc parents: 3 diff changeset	774 <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	775 <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	776 <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	777 </assert_contents>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	778 </output>
4 f97743d52b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386" iuc parents: 3 diff changeset	779 <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	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 <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	782 </assert_contents>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	783 </output>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	784 </test>
11 563c3aa769f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f" iuc parents: 10 diff changeset	785 <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	786 <!-- 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	787 <param name="seed" value="1257" />
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	788 <param name="seqtype" value="AA" />
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	789 <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	790 <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	791 <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	792 <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	793 <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	794 <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	795 <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	796 <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	797 <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	798 <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	799 <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	800 <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	801 <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	802 <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	803 <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	804 <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	805 <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	806 <param name="beps" value="0.5" />
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	807 <!-- <param name="b" value="100" /> -->
4 f97743d52b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386" iuc parents: 3 diff changeset	808 <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	809 <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	810 <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	811 </assert_contents>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	812 </output>
4 f97743d52b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386" iuc parents: 3 diff changeset	813 <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	814 <assert_contents>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	815 <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	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 </output>
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	818 </test>
11 563c3aa769f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f" iuc parents: 10 diff changeset	819 <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	820 <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	821 <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	822 <assert_contents>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	823 <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	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 </output>
4 f97743d52b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386" iuc parents: 3 diff changeset	826 <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	827 <assert_contents>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	828 <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	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 </output>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	831 </test>
11 563c3aa769f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f" iuc parents: 10 diff changeset	832 <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	833 <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	834 <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	835 <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	836 <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	837 <assert_contents>
973a28be3b7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 73ef23e40772952e5fde0576d66fa81de4916058" iuc parents: 2 diff changeset	838 <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	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 </output>
4 f97743d52b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386" iuc parents: 3 diff changeset	841 <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	842 <assert_contents>
973a28be3b7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 73ef23e40772952e5fde0576d66fa81de4916058" iuc parents: 2 diff changeset	843 <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	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 </output>
973a28be3b7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 73ef23e40772952e5fde0576d66fa81de4916058" iuc parents: 2 diff changeset	846 </test>
11 563c3aa769f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f" iuc parents: 10 diff changeset	847 <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	848 <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	849 <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	850 <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	851 <assert_contents>
fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	852 <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	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 </output>
4 f97743d52b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386" iuc parents: 3 diff changeset	855 </test>
11 563c3aa769f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f" iuc parents: 10 diff changeset	856 <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	857 <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	858 <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	859 <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	860 <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	861 <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	862 <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	863 <assert_contents>
524d31add34a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af" iuc parents: 6 diff changeset	864 <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	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 </output>
9 f58a10e2e46d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 00ddca12cd441fab5c928f93c62fa8aa79160967" iuc parents: 8 diff changeset	867 <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	868 <assert_contents>
f58a10e2e46d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 00ddca12cd441fab5c928f93c62fa8aa79160967" iuc parents: 8 diff changeset	869 <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	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 </output>
7 524d31add34a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af" iuc parents: 6 diff changeset	872 </test>
0 05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	873 </tests>
2 d1c340a5664b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 686710a7d313b828f1daed20c4055479727f2d91 iuc parents: 1 diff changeset	874 <help><![CDATA[
0 05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	875 IQ-TREE
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	876 =======
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	877
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	878 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	879
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	880 .. _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	881
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	882 General Tutorial
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	883 ===================
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	884
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	885 Input data
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
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	888 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	889
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	890 .. _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	891
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	892 ::
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 7 28
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	895 Frog AAATTTGGTCCTGTGATTCAGCAGTGAT
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	896 Turtle CTTCCACACCCCAGGACTCAGCAGTGAT
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	897 Bird CTACCACACCCCAGGACTCAGCAGTAAT
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	898 Human CTACCACACCCCAGGAAACAGCAGTGAT
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	899 Cow CTACCACACCCCAGGAAACAGCAGTGAC
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	900 Whale CTACCACGCCCCAGGACACAGCAGTGAT
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	901 Mouse CTACCACACCCCAGGACTCAGCAGTGAT
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	902
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	903 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	904
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	905 ::
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	906
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	907 >Frog
0 05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	908 AAATTTGGTCCTGTGATTCAGCAGTGAT
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	909 >Turtle
0 05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	910 CTTCCACACCCCAGGACTCAGCAGTGAT
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	911 >Bird
0 05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	912 CTACCACACCCCAGGACTCAGCAGTAAT
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	913 >Human
0 05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	914 CTACCACACCCCAGGAAACAGCAGTGAT
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	915 >Cow
0 05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	916 CTACCACACCCCAGGAAACAGCAGTGAC
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	917 >Whale
0 05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	918 CTACCACGCCCCAGGACACAGCAGTGAT
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	919 >Mouse
0 05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	920 CTACCACACCCCAGGACTCAGCAGTGAT
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	921
0 05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	922 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	923
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	924 .. _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	925 .. _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	926
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	927
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	928 Running example
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
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	931 From the download_ there is an example alignment called `example.phy`
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	932 in PHYLIP format. This example contains parts of the mitochondrial DNA sequences of several animals (Source: `Phylogenetic Handbook`_)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	933
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	934 .. _`Phylogenetic Handbook` : http://www.kuleuven.be/aidslab/phylogenybook/home.html)).
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	935 .. _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	936
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	937 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	938 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	939
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	940 ::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	941
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	942 * -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	943
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	944 * -st specifies the sequence type as amino-acid
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	945
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	946 * -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	947
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	948 * -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	949
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	950 * -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	951
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	952 * -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	953
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	954 * -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	955
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	956 * -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	957
0 05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	958
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	959 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	960
0 05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	961 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	962
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	963 * example.phy.iqtree: the main report file that is self-readable. You should look at this file to see the computational results. It also contains a textual representation of the final tree (see below).
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	964
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	965 * example.phy.treefile: the ML tree in NEWICK format, which can be visualized by any supported tree viewer programs like FigTree or iTOL.
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	966
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	967 NOTE: Starting with version 1.5.4, with this simple command IQ-TREE will by default perform ModelFinder to find the best-fit substitution model and then infer a phylogenetic tree using the selected model.
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	968
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	969 For this example data the resulting maximum-likelihood tree may look like this (extracted from .iqtree file):
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	970
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	971 NOTE: Tree is UNROOTED although outgroup taxon 'LngfishAu' is drawn at root
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	972
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	973 ::
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	974
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	975 +--------------LngfishAu
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	976 \|
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	977 \| +--------------LngfishSA
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	978 +--------\|
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	979 \| +--------------LngfishAf
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	980 \|
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	981 \| +-------------------Frog
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	982 +------\|
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	983 \| +-----------------Turtle
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	984 \| +-----\|
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	985 \| \| \| +-----------------------Sphenodon
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	986 \| \| \| +--\|
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	987 \| \| \| \| +--------------------------Lizard
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	988 \| \| +---\|
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	989 \| \| \| +---------------------Crocodile
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	990 \| \| +------\|
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	991 \| \| +------------------Bird
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	992 +---------\|
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	993 \| +----------------Human
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	994 \| +--\|
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	995 \| \| \| +--------Seal
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	996 \| \| +--\|
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	997 \| \| \| +-------Cow
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	998 \| \| +---\|
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	999 \| \| +---------Whale
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1000 \| +----\|
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1001 \| \| \| +------Mouse
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1002 \| \| +---------\|
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1003 \| \| +--------Rat
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1004 +----------\|
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1005 \| +----------------Platypus
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1006 +---\|
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	1007 +-------------Opossum
0 05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1008
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1009
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1010 This makes sense as the mammals (Human to Opossum) form a clade, whereas the reptiles Turtle to Crocodile) and Bird form a separate sister clade. Here the tree is drawn at the outgroup Lungfish which is more accient than other species in this example. However, please note that IQ-TREE always produces an unrooted tree as it knows nothing about this biological background; IQ-TREE simply draws the tree this way as LngfishAu is the first sequence occuring in the alignment.
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1011
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1012 Choosing the right substitution model
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1013 -------------------------------------
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1014
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1015 IQ-TREE will choose the best model for you automatically if specify any of the TEST models, but valid custom models can also be specified that conform to those found in Models_ page.
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1016
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1017 .. _Models: http://www.iqtree.org/doc/Substitution-Models#binary-and-morphological-models
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1018
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1019
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1020 ------------------------------
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1021
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1022 Advanced Parameter Selection
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1023 ============================
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1024
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1025 Using codon models
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1026 ------------------
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1027
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1028 IQ-TREE supports a number of codon models. You need to input a protein-coding DNA alignment and specify codon data by option -st CODON (Otherwise, IQ-TREE applies DNA model because it detects that your alignment has DNA sequences):
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1029
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1030 ::
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1031
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	1032 iqtree -s coding_gene.phy -st CODON
0 05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1033
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1034 If your alignment length is not divisible by 3, IQ-TREE will stop with an error message. IQ-TREE will group sites 1,2,3 into codon site 1; sites 4,5,6 to codon site 2; etc. Moreover, any codon, which has at least one gap/unknown/ambiguous nucleotide, will be treated as unknown codon character.
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1035
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1036 Note that the above command assumes the standard genetic code. If your sequences follow 'The Invertebrate Mitochondrial Code', then run:
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1037
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1038 ::
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	1039
288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	1040 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	1041
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1042 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	1043
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 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	1046 ----------------------------------------------------------------
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 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	1049
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	1050 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	1051
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
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	1054 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	1055
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	1056 -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	1057
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1058 * 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	1059
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1060 * 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	1061
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1062 * example.phy.splits.nex: has the same information as example.phy.splits but in NEXUS format, which can be viewed with the program SplitsTree_ to explore the conflicting signals in the data. So it is more informative than consensus tree, e.g. you can see how highly supported the second best conflicting split is, which had no chance to enter the consensus tree.
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1063
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1064 .. _SplitsTree: http://www.splitstree.org
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1065
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc 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 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	1068 ------------------------------------------------------
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 Starting with IQ-TREE version 1.6 we provide a new option -bnni to reduce the risk of overestimating branch supports with UFBoot due to severe model violations. With this option UFBoot will further optimize each bootstrap tree using a hill-climbing nearest neighbor interchange (NNI) search based directly on the corresponding bootstrap alignment.
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1071
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1072 Thus, if severe model violations are present in the data set at hand, users are advised to append -bnni to the regular UFBoot command:
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1073
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	1074 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 iuc parents: diff changeset	1075
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1076 For more details see:
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1077
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1078 D.T. Hoang, O. Chernomor, A. von Haeseler, B.Q. Minh, L.S. Vinh (2017) UFBoot2: Improving the ultrafast bootstrap approximation.
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1079
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: 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 Assessing branch supports with standard nonparametric bootstrap
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1082 ----------------------------------------------------------------
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: 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 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	1085
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1086 iqtree -s example.phy -m TIM2+I+G -b 100
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1087
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1088 -b specifies the number of bootstrap replicates where 100
1 288db50d1fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c iuc parents: 0 diff changeset	1089 is the minimum recommended number. The output files are similar to those produced by the UFBoot procedure.
0 05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1090
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: 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 Assessing branch supports with single branch tests
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1094 --------------------------------------------------
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1095
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1096 IQ-TREE provides an implementation of the SH-like approximate likelihood ratio test ([Guindon et al., 2010]). To perform this test, run:
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1097
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1098 ::
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1099
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	1100 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 iuc parents: diff changeset	1101
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	1102 --alrt specifies the number of bootstrap replicates for SH-aLRT where 1000 is the minimum number recommended.
0 05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1103
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1104 IQ-TREE also supports other tests such as the aBayes test (Anisimova et al., 2011) and the local bootstrap test (Adachi and Hasegawa, 1996).
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1105
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1106 You can also perform both SH-aLRT and the ultrafast bootstrap within one single run:
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1107
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1108 ::
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1109
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	1110 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 iuc parents: diff changeset	1111
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1112 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 iuc parents: diff changeset	1113
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1114 NOTE: Tree is UNROOTED although outgroup taxon 'LngfishAu' is drawn at root
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1115 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 iuc parents: diff changeset	1116
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1117 ::
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1118
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1119 +-------------LngfishAu
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1120 \|
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1121 \| +--------------LngfishSA
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1122 +-------\| (100/100)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1123 \| +------------LngfishAf
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1124 \|
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1125 \| +--------------------Frog
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1126 +------\| (99.8/100)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1127 \| +-----------------Turtle
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1128 \| +--\| (85/72)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1129 \| \| \| +------------------------Crocodile
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1130 \| \| +----\| (96.5/97)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1131 \| \| +------------------Bird
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1132 \| +--\| (39/51)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1133 \| \| +---------------------------Sphenodon
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1134 \| +-----\| (98.2/99)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1135 \| \| +-------------------------------Lizard
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1136 +---------\| (100/100)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1137 \| +--------------Human
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1138 \| +--\| (92.3/93)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1139 \| \| \| +------Seal
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1140 \| \| +--\| (68.3/75)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1141 \| \| \| +-----Cow
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1142 \| \| +--\| (99.7/100)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1143 \| \| +-------Whale
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1144 \| +----\| (99.1/100)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1145 \| \| \| +---Mouse
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1146 \| \| +---------\| (100/100)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1147 \| \| +------Rat
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1148 +-----------\| (100/100)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1149 \| +--------------Platypus
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1150 +--\| (93/98)
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1151 +-----------Opossum
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1152
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 parents: diff changeset	1154 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 iuc parents: 1 diff changeset	1155 ]]></help>
0 05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1156 <citations>
5 fc06db7794f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" iuc parents: 4 diff changeset	1157 <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 iuc parents: diff changeset	1158 <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	1159 <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	1160 <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	1161 <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	1162 <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	1163 <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	1164 </citations>
05ee0a74faef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1165 </tool>

Mercurial > repos > iuc > iqtree

annotate iqtree.xml @ 11:563c3aa769f2 draft