iqtree: iqtree.xml annotate

annotate iqtree.xml @ 0:72ef801e8d98 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997

author	iuc
date	Wed, 15 Nov 2017 12:45:06 -0500
parents
children	f041f5a855cc

rev	line source
0 72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	1 <tool id="iqtree" name="IQ-TREE" version="1.5.5" >
72ef801e8d98 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>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	3 <requirements>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	4 <requirement type="package" version="1.5.5">iqtree</requirement>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	5 </requirements>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	6 <command detect_errors='exit_code' ><![CDATA[
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	7 iqtree
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	8 -pre PREF
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	9 -nt AUTO
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	10 -redo
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	11
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	12 ## file
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	13 #if $general_options.s
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	14 -s '$general_options.s'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	15 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	16
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	17 ## file
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	18 #if $general_options.t
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	19 -t '$general_options.t'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	20 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	21
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	22 ## file
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	23 #if $general_options.te
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	24 -te '$general_options.te'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	25 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	26
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	27 #if str($general_options.st) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	28 -st '$general_options.st'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	29 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	30
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	31 #if str($general_options.seed) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	32 -seed '$general_options.seed'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	33 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	34
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	35 $general_options.keep_ident
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	36 $general_options.safe
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	37
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	38 #if str($likelihood_mapping.lmap) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	39 -lmap '$likelihood_mapping.lmap'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	40 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	41
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	42 ## file
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	43 #if $likelihood_mapping.lmclust
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	44 -lmclust '$likelihood_mapping.lmclust'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	45 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	46
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	47 $likelihood_mapping.wql
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	48
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	49 #if str($modelling_parameters.automatic_model.cond_model.m) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	50 -m '$modelling_parameters.automatic_model.cond_model.m'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	51 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	52
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	53 #if str($modelling_parameters.automatic_model.rcluster) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	54 -rcluster '$modelling_parameters.automatic_model.rcluster'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	55 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	56
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	57 #if str($modelling_parameters.automatic_model.mset) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	58 -mset '$modelling_parameters.automatic_model.mset'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	59 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	60
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	61 #if str($modelling_parameters.automatic_model.msub) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	62 -msub '$modelling_parameters.automatic_model.msub'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	63 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	64
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	65 #if str($modelling_parameters.automatic_model.mfreq) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	66 -mfreq '$modelling_parameters.automatic_model.mfreq'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	67 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	68
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	69 #if str($modelling_parameters.automatic_model.mrate) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	70 -mrate '$modelling_parameters.automatic_model.mrate'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	71 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	72
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	73 #if str($modelling_parameters.automatic_model.cmin) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	74 -cmin '$modelling_parameters.automatic_model.cmin'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	75 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	76
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	77 #if str($modelling_parameters.automatic_model.cmax) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	78 -cmax '$modelling_parameters.automatic_model.cmax'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	79 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	80
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	81 #if str($modelling_parameters.automatic_model.merit) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	82 -merit '$modelling_parameters.automatic_model.merit'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	83 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	84
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	85 $modelling_parameters.automatic_model.mtree
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	86
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	87 #if str($modelling_parameters.automatic_model.madd) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	88 -madd '$modelling_parameters.automatic_model.madd'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	89 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	90
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	91 ## file
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	92 #if $modelling_parameters.automatic_model.mdef
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	93 -mdef '$modelling_parameters.automatic_model.mdef'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	94 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	95
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	96 $modelling_parameters.specifying_substitution.mwopt
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	97
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	98 #if str($modelling_parameters.rate_heterogeneity.a) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	99 -a '$modelling_parameters.rate_heterogeneity.a'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	100 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	101
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	102 $modelling_parameters.rate_heterogeneity.gmedian
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	103
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	104 #if str($modelling_parameters.rate_heterogeneity.i) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	105 -i '$modelling_parameters.rate_heterogeneity.i'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	106 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	107
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	108 $modelling_parameters.rate_heterogeneity.opt_gamma_inv
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	109 $modelling_parameters.rate_heterogeneity.wsr
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	110
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	111 ## file
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	112 #if $modelling_parameters.partition_model.q
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	113 -q '$modelling_parameters.partition_model.q'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	114 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	115
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	116 $modelling_parameters.partition_model.spp
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	117
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	118 ## file
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	119 #if $modelling_parameters.partition_model.sp
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	120 -sp '$modelling_parameters.partition_model.sp'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	121 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	122
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	123 ## file
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	124 #if $modelling_parameters.site_specific_frequency.ft
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	125 -ft '$modelling_parameters.site_specific_frequency.ft'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	126 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	127
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	128 #if str($modelling_parameters.site_specific_frequency.fs) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	129 -fs '$modelling_parameters.site_specific_frequency.fs'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	130 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	131
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	132 $modelling_parameters.site_specific_frequency.fmax
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	133
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	134 #if str($tree_parameters.tree_search.ninit) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	135 -ninit '$tree_parameters.tree_search.ninit'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	136 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	137
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	138 #if str($tree_parameters.tree_search.ntop) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	139 -ntop '$tree_parameters.tree_search.ntop'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	140 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	141
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	142 #if str($tree_parameters.tree_search.nbest) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	143 -nbest '$tree_parameters.tree_search.nbest'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	144 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	145
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	146 #if str($tree_parameters.tree_search.nstop) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	147 -nstop '$tree_parameters.tree_search.nstop'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	148 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	149
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	150 #if str($tree_parameters.tree_search.n) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	151 -n '$tree_parameters.tree_search.n'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	152 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	153
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	154 #if str($tree_parameters.tree_search.sprrad) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	155 -sprrad '$tree_parameters.tree_search.sprrad'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	156 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	157
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	158 #if str($tree_parameters.tree_search.pers) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	159 -pers '$tree_parameters.tree_search.pers'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	160 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	161
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	162 $tree_parameters.tree_search.allnni
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	163 $tree_parameters.tree_search.djc
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	164
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	165 ## file
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	166 #if $tree_parameters.tree_search.g
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	167 -g '$tree_parameters.tree_search.g'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	168 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	169
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	170 #if str($tree_parameters.single_branch.alrt) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	171 -alrt '$tree_parameters.single_branch.alrt'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	172 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	173
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	174 $tree_parameters.single_branch.abayes
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	175
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	176 #if str($tree_parameters.single_branch.lbp) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	177 -lbp '$tree_parameters.single_branch.lbp'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	178 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	179
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	180 ## file
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	181 #if $tree_parameters.tree_topology.z
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	182 -z '$tree_parameters.tree_topology.z'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	183 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	184
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	185 #if str($tree_parameters.tree_topology.zb) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	186 -zb '$tree_parameters.tree_topology.zb'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	187 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	188
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	189 $tree_parameters.tree_topology.zw
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	190 $tree_parameters.tree_topology.au
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	191
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	192 $tree_parameters.constructing_consensus.con
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	193 $tree_parameters.constructing_consensus.net
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	194
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	195 #if str($tree_parameters.constructing_consensus.minsup) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	196 -minsup '$tree_parameters.constructing_consensus.minsup'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	197 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	198
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	199 #if str($tree_parameters.constructing_consensus.bi) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	200 -bi '$tree_parameters.constructing_consensus.bi'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	201 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	202
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	203 ## file
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	204 #if $tree_parameters.constructing_consensus.sup
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	205 -sup '$tree_parameters.constructing_consensus.sup'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	206 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	207
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	208 #if str($tree_parameters.constructing_consensus.suptag) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	209 -suptag '$tree_parameters.constructing_consensus.suptag'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	210 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	211
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	212 ## file
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	213 #if $tree_parameters.computing_robinson_foulds.rf
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	214 -rf '$tree_parameters.computing_robinson_foulds.rf'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	215 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	216
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	217 $tree_parameters.computing_robinson_foulds.rf_all
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	218 $tree_parameters.computing_robinson_foulds.rf_adj
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	219
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	220 #if str($tree_parameters.generating_random.r) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	221 -r '$tree_parameters.generating_random.r'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	222 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	223
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	224 $tree_parameters.generating_random.ru
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	225 $tree_parameters.generating_random.rcat
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	226 $tree_parameters.generating_random.rbal
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	227 $tree_parameters.generating_random.rcsg
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	228
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	229 #if str($tree_parameters.generating_random.rlen) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	230 -rlen '$tree_parameters.generating_random.rlen'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	231 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	232
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	233 #if str($bootstrap_parameters.ultrafast_bootstrap.bb) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	234 -bb '$bootstrap_parameters.ultrafast_bootstrap.bb'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	235 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	236
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	237 $bootstrap_parameters.ultrafast_bootstrap.wbt
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	238 $bootstrap_parameters.ultrafast_bootstrap.wbtl
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	239
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	240 #if str($bootstrap_parameters.ultrafast_bootstrap.nm) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	241 -nm '$bootstrap_parameters.ultrafast_bootstrap.nm'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	242 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	243
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	244 #if str($bootstrap_parameters.ultrafast_bootstrap.bcor) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	245 -bcor '$bootstrap_parameters.ultrafast_bootstrap.bcor'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	246 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	247
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	248 #if str($bootstrap_parameters.ultrafast_bootstrap.nstep) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	249 -nstep '$bootstrap_parameters.ultrafast_bootstrap.nstep'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	250 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	251
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	252 #if str($bootstrap_parameters.ultrafast_bootstrap.beps) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	253 -beps '$bootstrap_parameters.ultrafast_bootstrap.beps'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	254 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	255
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	256 #if str($bootstrap_parameters.ultrafast_bootstrap.bspec) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	257 -bspec '$bootstrap_parameters.ultrafast_bootstrap.bspec'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	258 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	259
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	260 $bootstrap_parameters.ultrafast_bootstrap.bnni
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	261
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	262 #if str($bootstrap_parameters.nonparametric_bootstrap.b) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	263 -b '$bootstrap_parameters.nonparametric_bootstrap.b'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	264 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	265
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	266 $bootstrap_parameters.nonparametric_bootstrap.bc
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	267 $bootstrap_parameters.nonparametric_bootstrap.bo
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	268
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	269 #if str($miscellaneous_options.fconst) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	270 -fconst '$miscellaneous_options.fconst'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	271 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	272
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	273 ]]>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	274 </command>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	275 <inputs>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	276 <section name="general_options" expanded="True" title="General options">
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	277 <param argument="-s" type="data" format="txt" optional="true" label="Specify input alignment file in PHYLIP, FASTA, NEXUS, CLUSTAL or MSF format."/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	278 <param argument="-st" type="select" label="Specify sequence type as either of DNA, AA, BIN, MORPH, CODON or NT2AA for DNA, amino-acid, binary, morphological, codon or DNA-to-AA-translated sequences">
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	279 <help><![CDATA[
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	280 Note that -st CODON is always necessary when using codon models and you also need to specify a genetic code like this if differed from the standard genetic code.
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	281 <br /><i>-st</i> NT2AA tells IQ-TREE to translate protein-coding DNA into AA sequences and then subsequent analysis will work on the AA sequences. You can also use a genetic code like -st NT2AA5 for the Invertebrate Mitochondrial Code (see genetic code table).]]>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	282 </help>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	283 <option value="DNA">DNA</option>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	284 <option value="AA">AA</option>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	285 <option value="BIN">BIN</option>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	286 <option value="MORPH">MORPH</option>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	287 <option value="CODON">CODON</option>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	288 <option value="NT2AA">NT2AA</option>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	289 </param>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	290 <param argument="-t" type="data" format="nhx" optional="true" label="Specify a file containing starting tree for tree search"/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	291 <param argument="-te" type="data" format="nhx" optional="true" label="Like -t but fixing user tree" help="That means, no tree search is performed and IQ-TREE computes the log-likelihood of the fixed user tree."/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	292 <param argument="-seed" type="integer" optional="true" label="Specify a random number seed to reproduce a previous run (leave blank to randomize)"/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	293 <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."/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	294 <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."/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	295 </section>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	296 <section name="likelihood_mapping" expanded="False" title="Likelihood mapping analysis">
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	297 <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."/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	298 <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."/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	299 <param argument="-wql" type="boolean" truevalue="-wql" falsevalue="" checked="false" label="Write quartet log-likelihoods into .lmap.quartetlh file (typically not needed)."/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	300 </section>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	301 <section name="modelling_parameters" title="Modelling Parameters">
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	302 <section name="automatic_model" expanded="False" title="Automatic model selection">
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	303 <conditional name="cond_model" >
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	304 <param name="opt_custommodel" type="boolean" checked="false" label="Use Custom Model" help="See http://www.iqtree.org/doc/Substitution-Models"/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	305 <when value="true">
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	306 <param argument="-m" type="text" label="Model">
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	307 <sanitizer>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	308 <valid initial="string.ascii_uppercase,+" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	309 </sanitizer>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	310 </param>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	311 </when>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	312 <when value="false">
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	313 <param argument="-m" type="select" label="Perform standard model selection like jModelTest (for DNA) and ProtTest (for protein)" >
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	314 <help><![CDATA[
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	315 Moreover, IQ-TREE also works for codon, binary and morphogical data.
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	316 <table>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	317 <tr>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	318 <td><i>TESTONLY</i></td>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	319 <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>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	320 </tr>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	321 <tr>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	322 <td><i>TEST</i></td>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	323 <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>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	324 </tr>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	325 <tr>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	326 <td><i>TESTNEWONLY</i></td>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	327 <td>Perform an extended model selection that additionally includes FreeRate model compared with -m TESTONLY. Recommended as replacement for -m TESTONLY. Note that LG4X is a FreeRate model, but by default is not included because it is also a protein mixture model. To include it, use -madd option (see table below).</td>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	328 </tr>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	329 <tr>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	330 <td><i>TESTNEW</i></td>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	331 <td>Like -m MF but immediately followed by tree reconstruction using the best-fit model found.</td>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	332 </tr>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	333 <tr>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	334 <td><i>TESTMERGEONLY</i></td>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	335 <td>Select best-fit partitioning scheme like PartitionFinder.</td>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	336 </tr>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	337 <tr>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	338 <td><i>TESTMERGE</i></td>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	339 <td>Like -m TESTMERGEONLY but immediately followed by tree reconstruction using the best partitioning scheme found.</td>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	340 </tr>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	341 <tr>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	342 <td><i>TESTNEWMERGEONLY</i></td>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	343 <td>Like -m TESTMERGEONLY but additionally includes FreeRate model.</td>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	344 </tr>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	345 <tr>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	346 <td><i>TESTNEWMERGE</i></td>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	347 <td>Like -m MF+MERGE but immediately followed by tree reconstruction using the best partitioning scheme found.</td>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	348 </tr>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	349 </table>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	350 ]]>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	351 </help>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	352 <option value="TESTONLY">TESTONLY</option>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	353 <option value="TEST">TEST</option>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	354 <option value="TESTNEWONLY">TESTNEWONLY</option>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	355 <option value="TESTNEW">TESTNEW</option>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	356 <option value="TESTMERGEONLY">TESTMERGEONLY</option>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	357 <option value="TESTMERGE">TESTMERGE</option>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	358 <option value="TESTNEWMERGEONLY">TESTNEWMERGEONLY</option>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	359 <option value="TESTNEWMERGE">TESTNEWMERGE</option>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	360 </param>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	361 </when>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	362 </conditional>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	363 <param argument="-rcluster" type="integer" optional="true" label="Specify the percentage for the relaxed clustering algorithm (Lanfear et al., 2014)" help="This is similar to --rcluster-percent option of PartitionFinder. For example, with -rcluster 10 only the top 10% partition schemes are considered to save computations." />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	364 <param argument="-mset" type="text" optional="true" label="Specify the name of a program (raxml, phyml or mrbayes) to restrict to only those models supported by the specified program" help="Alternatively, one can specify a comma-separated list of base models. For example, -mset WAG,LG,JTT will restrict model selection to WAG, LG, and JTT instead of all 18 AA models to save computations.">
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	365 <sanitizer>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	366 <valid initial="string.ascii_uppercase,string.punctuation" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	367 </sanitizer>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	368 </param>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	369 <param argument="-msub" type="select" label="Specify either nuclear, mitochondrial, chloroplast or viral to restrict to those AA models designed for specified source." help="">
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	370 <option value="nuclear">nuclear</option>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	371 <option value="mitochondrial">mitochondrial</option>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	372 <option value="chloroplast">chloroplast</option>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	373 <option value="viral">viral</option>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	374 </param>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	375 <param argument="-mfreq" type="text" optional="true" label="Specify a comma-separated list of frequency types for model selection" >
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	376 <sanitizer>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	377 <valid initial="string.ascii_uppercase,string.digits,x,string.punctuation" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	378 </sanitizer>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	379 </param>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	380 <param argument="-mrate" type="text" optional="true" label="Specify a comma-separated list of rate heterogeneity types for model selection">
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	381 <sanitizer>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	382 <valid initial="string.ascii_uppercase,string.punctuation" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	383 </sanitizer>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	384 </param>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	385 <param argument="-cmin" type="integer" value="2" optional="true" label="Specify minimum number of categories for FreeRate model"/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	386 <param argument="-cmax" type="integer" value="10" optional="true" label="Specify maximum number of categories for FreeRate model"/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	387 <param argument="-merit" type="select" label="Specify either AIC, AICc or BIC for the optimality criterion to apply for new procedure" help="">
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	388 <option value="AIC">AIC</option>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	389 <option value="AICc">AICc</option>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	390 <option value="BIC">BIC</option>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	391 </param>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	392 <param argument="-mtree" type="boolean" truevalue="-mtree" falsevalue="" checked="false" label="Turn on full tree search for each model considered, to obtain more accurate result"/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	393 <param argument="-madd" type="text" optional="true" label="Specify a comma-separated list of mixture models to additionally consider for model selection" help="For example, -madd LG4M,LG4X to additionally include these two protein mixture models.">
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	394 <sanitizer>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	395 <valid initial="string.ascii_uppercase,string.digits,string.punctuation" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	396 </sanitizer>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	397 </param>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	398 <param argument="-mdef" type="data" format="txt" optional="true" label="Specify a NEXUS model file to define new models."/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	399 </section>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	400 <section name="specifying_substitution" expanded="False" title="Specifying substitution models">
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	401 <param argument="-mwopt" type="boolean" truevalue="-mwopt" falsevalue="" checked="false" label="Turn on optimizing weights of mixture models" help="Note that for models like LG+C20+F+G this mode is automatically turned on, but not for LG+C20+G."/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	402 </section>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	403 <section name="rate_heterogeneity" expanded="False" title="Rate heterogeneity">
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	404 <param argument="-a" type="text" optional="true" label="Specify the Gamma shape parameter (default: estimate)">
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	405 <sanitizer>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	406 <valid initial="string.printable" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	407 </sanitizer>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	408 </param>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	409 <param argument="-gmedian" type="boolean" truevalue="-gmedian" falsevalue="" checked="false" label="Perform the median approximation for Gamma rate heterogeneity instead of the default mean approximation (Yang, 1994)"/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	410 <param argument="-i" type="text" optional="true" label="Specify the proportion of invariable sites (default: estimate)">
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	411 <sanitizer>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	412 <valid initial="string.printable" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	413 </sanitizer>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	414 </param>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	415 <param argument="--opt_gamma_inv" type="boolean" truevalue="--opt-gamma-inv" falsevalue="" checked="false" label="Perform more thorough estimation for +I+G model parameters"/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	416 <param argument="-wsr" type="boolean" truevalue="-wsr" falsevalue="" checked="false" label="Write per-site rates to .rate file"/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	417 </section>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	418 <section name="partition_model" expanded="False" title="Partition model options">
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	419 <param argument="-q" type="data" format="txt" optional="true" label="Specify partition file for edge-equal partition model" help="That means, all partitions share the same set of branch lengths (like -q option of RAxML)."/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	420 <param argument="-spp" type="boolean" truevalue="-spp" falsevalue="" checked="false" label="Like -q but allowing partitions to have different evolutionary speeds (edge-proportional partition model)."/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	421 <param argument="-sp" type="data" format="txt" optional="true" label="Specify partition file for edge-unlinked partition model" help="That means, each partition has its own set of branch lengths (like -M option of RAxML). This is the most parameter-rich partition model to accomodate heterotachy."/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	422 </section>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	423 <section name="site_specific_frequency" expanded="False" title="Site-specific frequency model options">
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	424 <param argument="-ft" type="data" format="nhx" optional="true" label="Specify a guide tree to infer site frequency profiles."/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	425 <param argument="-fs" type="float" optional="true" label="Specify a site frequency file, e.g" help="the .sitefreq file obtained from -ft run. This will save memory used for the first phase of the analysis."/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	426 <param argument="-fmax" type="boolean" truevalue="-fmax" falsevalue="" checked="false" label="Switch to posterior maximum mode for obtaining site-specific profiles" help="Default: posterior mean."/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	427 </section>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	428 </section>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	429 <section name="tree_parameters" title="Tree Parameters">
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	430 <section name="tree_search" expanded="False" title="Tree search parameters">
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	431 <param argument="-n" type="integer" optional="true" label="Skip subsequent tree search (n = 0), useful when you only want to assess the phylogenetic information of the alignment. Otherwise specify number of iterations to stop (this option overrides -nstop criterion)." />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	432 <param argument="-ninit" type="integer" value="100" optional="true" label="Specify number of initial parsimony trees"/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	433 <param argument="-ntop" type="integer" value="20" optional="true" label="Specify number of top initial parsimony trees to optimize with ML nearest neighbor interchange (NNI) search to initialize the candidate set"/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	434 <param argument="-nbest" type="integer" value="5" optional="true" label="Specify number of trees in the candidate set to maintain during ML tree search"/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	435 <param argument="-nstop" type="integer" value="100" optional="true" label="Specify number of unsuccessful iterations to stop"/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	436 <param argument="-sprrad" type="integer" value="6" optional="true" label="Specify SPR radius for the initial parsimony tree search"/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	437 <param argument="-pers" type="float" value="0.5" optional="true" label="Specify perturbation strength (between 0 and 1) for randomized NNI"/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	438 <param argument="-allnni" type="boolean" truevalue="-allnni" falsevalue="" checked="false" label="Turn on more thorough and slower NNI search"/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	439 <param argument="-djc" type="boolean" truevalue="-djc" falsevalue="" checked="false" label="Avoid computing ML pairwise distances and BIONJ tree."/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	440 <param argument="-g" type="data" format="txt" optional="true" label="Specify a topological constraint tree file in NEWICK format" help="The constraint tree can be a multifurcating tree and need not to include all taxa."/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	441 </section>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	442 <section name="single_branch" expanded="False" title="Single branch tests">
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	443 <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."/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	444 <param argument="-abayes" type="boolean" truevalue="-abayes" falsevalue="" checked="false" label="Perform approximate Bayes test (Anisimova et al., 2011)."/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	445 <param argument="-lbp" type="integer" optional="true" label="Specify number of replicates (>=1000) to perform fast local bootstrap probability method (Adachi and Hasegawa, 1996)."/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	446 </section>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	447 <section name="tree_topology" expanded="False" title="Tree topology tests">
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	448 <param argument="-z" type="data" format="txt" optional="true" label="Specify a file containing a set of trees" help="IQ-TREE will compute the log-likelihoods of all trees."/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	449 <param argument="-zb" 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)."/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	450 <param argument="-zw" type="boolean" truevalue="-zw" falsevalue="" checked="false" label="Used together with -zb to additionally perform the weighted-KH and weighted-SH tests."/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	451 <param argument="-au" type="boolean" truevalue="-au" falsevalue="" checked="false" label="Used together with -zb to additionally perform the approximately unbiased (AU) test (Shimodaira, 2002)" help="Note that you have to specify the number of replicates for the AU test via -zb."/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	452 </section>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	453 <section name="constructing_consensus" expanded="False" title="Constructing consensus tree">
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	454 <param argument="-con" type="boolean" truevalue="-con" falsevalue="" checked="false" label="Compute consensus tree of the trees passed via -t" help="Resulting consensus tree is written to .contree file."/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	455 <param argument="-net" type="boolean" truevalue="-net" falsevalue="" checked="false" label="Compute consensus network of the trees passed via -t" help="Resulting consensus network is written to .nex file."/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	456 <param argument="-minsup" type="float" value="0.0" optional="true" label="Specify a minimum threshold (between 0 and 1) to keep branches in the consensus tree"/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	457 <param argument="-bi" type="integer" optional="true" label="Specify a burn-in, which is the number of beginning trees passed via -t to discard before consensus construction" help="This is useful e.g. when summarizing trees from MrBayes analysis."/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	458 <param argument="-sup" type="data" format="nhx" optional="true" label="Specify an input “target” tree file" help="That means, support values are first extracted from the trees passed via -t, and then mapped onto the target tree. Resulting tree with assigned support values is written to .suptree file. This option is useful to map and compare support values from different approaches onto a single tree."/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	459 <param argument="-suptag" type="text" optional="true" label="Specify name of a node in -sup target tree" help="The corresponding node of .suptree will then be assigned with IDs of trees where this node appears. Special option -suptag ALL will assign such IDs for all nodes of the target tree."/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	460 </section>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	461 <section name="computing_robinson_foulds" expanded="False" title="Computing Robinson-Foulds distance">
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	462 <param argument="-rf" type="data" format="nhx" optional="true" label="Specify a second set of trees" help="IQ-TREE computes all pairwise RF distances between two tree sets passed via -t and -rf"/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	463 <param argument="-rf_all" type="boolean" truevalue="-rf_all" falsevalue="" checked="false" label="Compute all-to-all RF distances between all trees passed via -t"/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	464 <param argument="-rf_adj" type="boolean" truevalue="-rf_adj" falsevalue="" checked="false" label="Compute RF distances between adjacent trees passed via -t"/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	465 </section>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	466 <section name="generating_random" expanded="False" title="Generating random trees">
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	467 <param argument="-r" type="integer" optional="true" label="Specify number of taxa" help="IQ-TREE will create a random tree under Yule-Harding model with specified number of taxa"/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	468 <param argument="-ru" type="boolean" truevalue="-ru" falsevalue="" checked="false" label="Like -r, but a random tree is created under uniform model."/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	469 <param argument="-rcat" type="boolean" truevalue="-rcat" falsevalue="" checked="false" label="Like -r, but a random caterpillar tree is created."/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	470 <param argument="-rbal" type="boolean" truevalue="-rbal" falsevalue="" checked="false" label="Like -r, but a random balanced tree is created."/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	471 <param argument="-rcsg" type="boolean" truevalue="-rcsg" falsevalue="" checked="false" label="Like -r, bur a random circular split network is created."/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	472 <param argument="-rlen" type="text" optional="true" label="Specify three numbers: minimum, mean and maximum branch lengths of the random tree">
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	473 <sanitizer>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	474 <valid initial="string.digits,string.whitespace" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	475 </sanitizer>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	476 </param>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	477 </section>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	478 </section>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	479 <section name="bootstrap_parameters" title="Bootstrap Parameters">
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	480 <section name="ultrafast_bootstrap" expanded="False" title="Ultrafast bootstrap parameters">
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	481 <param argument="-bb" type="integer" optional="true" label="Specify number of bootstrap replicates (>=1000)."/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	482 <param argument="-wbt" type="boolean" truevalue="-wbt" falsevalue="" checked="false" label="Turn on writing bootstrap trees to .ufboot file"/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	483 <param argument="-wbtl" type="boolean" truevalue="-wbtl" falsevalue="" checked="false" label="Like -wbt but bootstrap trees written with branch lengths"/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	484 <param argument="-nm" type="integer" value="1000" optional="true" label="Specify maximum number of iterations to stop"/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	485 <param argument="-bcor" type="float" value="0.99" optional="true" label="Specify minimum correlation coefficient for UFBoot convergence criterion"/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	486 <param argument="-nstep" type="integer" value="100" optional="true" label="Specify iteration interval checking for UFBoot convergence"/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	487 <param argument="-beps" type="float" value="0.5" optional="true" label="Specify a small epsilon to break tie in RELL evaluation for bootstrap trees"/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	488 <param argument="-bspec" type="text" optional="true" label="Specify the resampling strategies for partitioned analysis" help="By default, IQ-TREE resamples alignment sites within partitions. With -bspec GENE IQ-TREE will resample partitions. With -bspec GENESITE IQ-TREE will resample partitions and then resample sites within resampled partitions (Gadagkar et al., 2005).">
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	489 <sanitizer>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	490 <valid initial="string.ascii_uppercase" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	491 </sanitizer>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	492 </param>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	493 <param argument="-bnni" type="boolean" truevalue="-bnni" falsevalue="" checked="false" label="Perform an additional step to further optimize UFBoot trees by nearest neighbor interchange (NNI) based directly on bootstrap alignments" help="This option is recommended in the presence of severe model violations. It increases computing time by 2-fold but reduces the risk of overestimating branch supports due to severe model violations. Introduced in IQ-TREE 1.6."/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	494 </section>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	495 <section name="nonparametric_bootstrap" expanded="False" title="Nonparametric bootstrap">
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	496 <param argument="-b" type="integer" optional="true" label="Specify number of bootstrap replicates (recommended >=100)" help="This will perform both bootstrap and analysis on original alignment and provide a consensus tree."/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	497 <param argument="-bc" type="boolean" truevalue="-bc" falsevalue="" checked="false" label="Like -b but omit analysis on original alignment."/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	498 <param argument="-bo" type="boolean" truevalue="-bo" falsevalue="" checked="false" label="Like -b but only perform bootstrap analysis (no analysis on original alignment and no consensus tree)."/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	499 </section>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	500 </section>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	501 <section name="miscellaneous_options" expanded="False" title="Miscellaneous options">
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	502 <param argument="-fconst" type="text" optional="true" label="Specify a list of comma-separated integer numbers" help="The number of entries should be equal to the number of states in the model (e.g. 4 for DNA and 20 for protein). IQ-TREE will then add a number of constant sites accordingly. For example, -fconst 10,20,15,40 will add 10 constant sites of all A, 20 constant sites of all C, 15 constant sites of all G and 40 constant sites of all T into the alignment.">
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	503 <sanitizer>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	504 <valid initial="string.digits,string.punctuation" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	505 </sanitizer>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	506 </param>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	507 </section>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	508 </inputs>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	509 <outputs>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	510 <data name='bionj' format='nhx' from_work_dir="*.bionj" label="${tool.name} on ${on_string}: BIONJ Tree" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	511 <data name='treefile' format='nhx' from_work_dir="*.treefile" label="${tool.name} on ${on_string}: MaxLikelihood Tree" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	512 <data name='contree' format='nhx' from_work_dir="*.contree" label="${tool.name} on ${on_string}: Consensus Tree" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	513 <data name='mldist' format='mldist' from_work_dir="*.mldist" label="${tool.name} on ${on_string}: MaxLikelihood Distance Matrix"/>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	514 <data name='splits.nex' format='nex' from_work_dir="*.splits.nex" label="${tool.name} on ${on_string}: Occurence Frequencies in Bootstrap Trees" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	515 <data name='iqtree' format='iqtree' from_work_dir="*.iqtree" label="${tool.name} on ${on_string}: Report and Final Tree" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	516 </outputs>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	517 <tests>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	518 <test>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	519 <param name="seed" value="1257" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	520 <param name="st" value="AA" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	521 <param name="s" value="example.phy" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	522 <param name="m" value="TESTNEW" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	523 <param name="msub" value="nuclear" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	524 <param name="madd" value="LG4M,LG4X" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	525 <param name="merit" value="AICc" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	526 <param name="bb" value="2000" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	527 <output name='bionj'>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	528 <assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	529 <has_text_matching expression=".Human.Whale.*" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	530 </assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	531 </output>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	532 <output name='iqtree'>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	533 <assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	534 <has_text_matching expression="VT\+F\+R3(\s+((-\|\d\|\.)+))+" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	535 </assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	536 </output>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	537 <output name='mldist'>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	538 <assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	539 <has_line_matching expression="^Frog(\s+((\d\|\.)+))+\s+$" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	540 <has_line_matching expression="^Whale(\s+((\d\|\.)+))+\s+$" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	541 <has_line_matching expression="^Cow(\s+((\d\|\.)+))+\s+$" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	542 </assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	543 </output>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	544 <output name='treefile'>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	545 <assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	546 <has_line_matching expression="\(LngfishAu:(\d\|\..)+,\(LngfishSA:(\d.)+,.*" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	547 </assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	548 </output>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	549 <output name='contree' >
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	550 <assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	551 <has_line_matching
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	552 expression="$LngfishAu:(\d\|\..)+,\(LngfishSA:(\d.)+,.$\d+:(\d\|\.)+,." />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	553 </assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	554 </output>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	555 <output name='splits.nex'>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	556 <assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	557 <has_line line="BEGIN Splits;" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	558 <has_line line="END; [Splits]" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	559 </assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	560 </output>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	561 </test>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	562 <test>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	563 <param name='s' value='example.phy' />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	564 <output name='iqtree'>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	565 <assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	566 <has_text_matching expression=".Human.Whale.*" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	567 </assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	568 </output>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	569 <output name='treefile'>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	570 <assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	571 <has_text_matching expression="\(LngfishAu:(\d\|\..)+,\(LngfishSA:(\d.)+,.*" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	572 </assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	573 </output>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	574 </test>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	575 </tests>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	576 <help>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	577 IQ-TREE
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	578 =======
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	579
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	580 The full documentation can be found here_.
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	581
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	582 .. _here : http://www.iqtree.org/doc/
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	583
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	584 General Tutorial
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	585 ===================
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	586
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	587 Input data
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	588 ----------
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	589
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	590 IQ-TREE takes as input a multiple sequence alignment and will reconstruct an evolutionary tree that is best explained by the input data. The input alignment can be in various common formats. For example the PHYLIP_ format which may look like:
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	591
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	592 .. _PHYLIP: http://evolution.genetics.washington.edu/phylip/doc/sequence.html
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	593
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	594 ::
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	595
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	596 7 28
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	597 Frog AAATTTGGTCCTGTGATTCAGCAGTGAT
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	598 Turtle CTTCCACACCCCAGGACTCAGCAGTGAT
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	599 Bird CTACCACACCCCAGGACTCAGCAGTAAT
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	600 Human CTACCACACCCCAGGAAACAGCAGTGAT
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	601 Cow CTACCACACCCCAGGAAACAGCAGTGAC
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	602 Whale CTACCACGCCCCAGGACACAGCAGTGAT
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	603 Mouse CTACCACACCCCAGGACTCAGCAGTGAT
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	604
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	605 This tiny alignment contains 7 DNA sequences from several animals with the sequence length of 28 nucleotides. IQ-TREE also supports other file formats such as FASTA, NEXUS, CLUSTALW. The FASTA file for the above example may look like this:
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	606
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	607 ::
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	608
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	609 >Frog
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	610 AAATTTGGTCCTGTGATTCAGCAGTGAT
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	611 >Turtle
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	612 CTTCCACACCCCAGGACTCAGCAGTGAT
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	613 >Bird
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	614 CTACCACACCCCAGGACTCAGCAGTAAT
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	615 >Human
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	616 CTACCACACCCCAGGAAACAGCAGTGAT
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	617 >Cow
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	618 CTACCACACCCCAGGAAACAGCAGTGAC
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	619 >Whale
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	620 CTACCACGCCCCAGGACACAGCAGTGAT
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	621 >Mouse
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	622 CTACCACACCCCAGGACTCAGCAGTGAT
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	623
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	624 NOTE: If you have raw sequences, you need to first apply alignment programs like MAFFT_ or ClustalW_ to align the sequences, before feeding them into IQ-TREE.
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	625
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	626 .. _MAFFT: http://mafft.cbrc.jp/alignment/software/
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	627 .. _ClustalW: http://www.clustal.org
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	628
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	629
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	630 Running example
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	631 ---------------------
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	632
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	633 From the download_ there is an example alignment called `example.phy`
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	634 in PHYLIP format. This example contains parts of the mitochondrial DNA sequences of several animals (Source: `Phylogenetic Handbook`_)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	635
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	636 .. _`Phylogenetic Handbook` : http://www.kuleuven.be/aidslab/phylogenybook/home.html)).
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	637 .. _download: http://www.iqtree.org/#download
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	638
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	639 You can now start to reconstruct a maximum-likelihood tree
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	640 from this alignment by entering (assuming that you are now in the same folder with `example.phy`):
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	641
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	642 ::iqtree -s example.phy -st AA -seed 9999 -m TESTNEW -msub nuclear -madd LG4M,LG4x -merit AICc -bb 2000
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	643
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	644 * -s is the option to specify the name of the alignment file
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	645
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	646 * -st specifies the sequence type as amino-acid
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	647
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	648 * -seed ensures that the output files remain the same for subsequent runs
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	649
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	650 * -m sets the modelling parameter for standard model selection
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	651
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	652 * -msub determines the type sub-modelling
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	653
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	654 * -madd provides an additional selection mixed models
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	655
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	656 * -merit asserts the type of optimality criterion
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	657
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	658 * -bb defines the number of replicates
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	659
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	660
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	661 Each of these parameters are available under the relevant sub-sections in the main tool interface.
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	662
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	663 At the end of the run IQ-TREE will write several output files including:
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	664
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	665 * example.phy.iqtree: the main report file that is self-readable. You should look at this file to see the computational results. It also contains a textual representation of the final tree (see below).
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	666
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	667 * example.phy.treefile: the ML tree in NEWICK format, which can be visualized by any supported tree viewer programs like FigTree or iTOL.
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	668
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	669 NOTE: Starting with version 1.5.4, with this simple command IQ-TREE will by default perform ModelFinder to find the best-fit substitution model and then infer a phylogenetic tree using the selected model.
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	670
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	671 For this example data the resulting maximum-likelihood tree may look like this (extracted from .iqtree file):
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	672
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	673 NOTE: Tree is UNROOTED although outgroup taxon 'LngfishAu' is drawn at root
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	674
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	675 ::
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	676
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	677 +--------------LngfishAu
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	678 \|
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	679 \| +--------------LngfishSA
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	680 +--------\|
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	681 \| +--------------LngfishAf
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	682 \|
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	683 \| +-------------------Frog
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	684 +------\|
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	685 \| +-----------------Turtle
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	686 \| +-----\|
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	687 \| \| \| +-----------------------Sphenodon
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	688 \| \| \| +--\|
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	689 \| \| \| \| +--------------------------Lizard
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	690 \| \| +---\|
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	691 \| \| \| +---------------------Crocodile
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	692 \| \| +------\|
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	693 \| \| +------------------Bird
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	694 +---------\|
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	695 \| +----------------Human
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	696 \| +--\|
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	697 \| \| \| +--------Seal
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	698 \| \| +--\|
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	699 \| \| \| +-------Cow
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	700 \| \| +---\|
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	701 \| \| +---------Whale
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	702 \| +----\|
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	703 \| \| \| +------Mouse
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	704 \| \| +---------\|
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	705 \| \| +--------Rat
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	706 +----------\|
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	707 \| +----------------Platypus
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	708 +---\|
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	709 +-------------Opossum
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	710
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	711
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	712 This makes sense as the mammals (Human to Opossum) form a clade, whereas the reptiles Turtle to Crocodile) and Bird form a separate sister clade. Here the tree is drawn at the outgroup Lungfish which is more accient than other species in this example. However, please note that IQ-TREE always produces an unrooted tree as it knows nothing about this biological background; IQ-TREE simply draws the tree this way as LngfishAu is the first sequence occuring in the alignment.
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	713
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	714 Choosing the right substitution model
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	715 -------------------------------------
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	716
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	717 IQ-TREE will choose the best model for you automatically if specify any of the TEST models, but valid custom models can also be specified that conform to those found in Models_ page.
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	718
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	719 .. _Models: http://www.iqtree.org/doc/Substitution-Models#binary-and-morphological-models
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	720
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	721
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	722 ------------------------------
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	723
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	724 Advanced Parameter Selection
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	725 ============================
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	726
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	727 Using codon models
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	728 ------------------
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	729
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	730 IQ-TREE supports a number of codon models. You need to input a protein-coding DNA alignment and specify codon data by option -st CODON (Otherwise, IQ-TREE applies DNA model because it detects that your alignment has DNA sequences):
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	731
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	732 ::
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	733
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	734 iqtree -s coding_gene.phy -st CODON
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	735
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	736 If your alignment length is not divisible by 3, IQ-TREE will stop with an error message. IQ-TREE will group sites 1,2,3 into codon site 1; sites 4,5,6 to codon site 2; etc. Moreover, any codon, which has at least one gap/unknown/ambiguous nucleotide, will be treated as unknown codon character.
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	737
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	738 Note that the above command assumes the standard genetic code. If your sequences follow 'The Invertebrate Mitochondrial Code', then run:
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	739
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	740 ::
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	741
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	742 iqtree -s coding_gene.phy -st CODON5
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	743
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	744 Note that ModelFinder works for codon alignments. IQ-TREE version >= 1.5.4 will automatically invokes ModelFinder to find the best-fit codon model.
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	745
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	746
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	747 Assessing branch supports with ultrafast bootstrap approximation
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	748 ----------------------------------------------------------------
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	749
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	750 To overcome the computational burden required by the nonparametric bootstrap, IQ-TREE introduces an ultrafast bootstrap approximation (UFBoot) ([Minh et al., 2013]) that is orders of magnitude faster than the standard procedure and provides relatively unbiased branch support values. Citation for UFBoot:
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	751
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	752 B.Q. Minh, M.A.T. Nguyen, and A. von Haeseler (2013) Ultrafast approximation for phylogenetic bootstrap. _Mol. Biol. Evol., 30:1188-1195.
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	753
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	754 ::
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	755
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	756 iqtree -s example.phy -m TIM2+I+G -bb 1000
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	757
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	758 -bb specifies the number of bootstrap replicates where 1000 is the minimum number recommended. The section MAXIMUM LIKELIHOOD TREE in example.phy.iqtree shows a textual representation of the maximum likelihood tree with branch support values in percentage. The NEWICK format of the tree is printed to the file example.phy.treefile. In addition, IQ-TREE writes the following files:
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	759
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	760 * example.phy.contree: the consensus tree with assigned branch supports where branch lengths are optimized on the original alignment.
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	761
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	762 * example.phy.splits: support values in percentage for all splits (bipartitions), computed as the occurence frequencies in the bootstrap trees. This file is in "star-dot" format.
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	763
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	764 * example.phy.splits.nex: has the same information as example.phy.splits but in NEXUS format, which can be viewed with the program SplitsTree_ to explore the conflicting signals in the data. So it is more informative than consensus tree, e.g. you can see how highly supported the second best conflicting split is, which had no chance to enter the consensus tree.
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	765
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	766 .. _SplitsTree: http://www.splitstree.org
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	767
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	768
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	769 Reducing impact of severe model violations with UFBoot
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	770 ------------------------------------------------------
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	771
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	772 Starting with IQ-TREE version 1.6 we provide a new option -bnni to reduce the risk of overestimating branch supports with UFBoot due to severe model violations. With this option UFBoot will further optimize each bootstrap tree using a hill-climbing nearest neighbor interchange (NNI) search based directly on the corresponding bootstrap alignment.
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	773
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	774 Thus, if severe model violations are present in the data set at hand, users are advised to append -bnni to the regular UFBoot command:
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	775
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	776 iqtree -s example.phy -m TIM2+I+G -bb 1000 -bnni
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	777
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	778 For more details see:
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	779
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	780 D.T. Hoang, O. Chernomor, A. von Haeseler, B.Q. Minh, L.S. Vinh (2017) UFBoot2: Improving the ultrafast bootstrap approximation.
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	781
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	782
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	783 Assessing branch supports with standard nonparametric bootstrap
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	784 ----------------------------------------------------------------
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	785
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	786 The standard nonparametric bootstrap is invoked by the -b option:
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	787
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	788 iqtree -s example.phy -m TIM2+I+G -b 100
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	789
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	790 -b specifies the number of bootstrap replicates where 100
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	791 is the minimum recommended number. The output files are similar to those produced by the UFBoot procedure.
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	792
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	793
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	794
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	795 Assessing branch supports with single branch tests
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	796 --------------------------------------------------
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	797
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	798 IQ-TREE provides an implementation of the SH-like approximate likelihood ratio test ([Guindon et al., 2010]). To perform this test, run:
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	799
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	800 ::
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	801
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	802 iqtree -s example.phy -m TIM2+I+G -alrt 1000
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	803
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	804 -alrt specifies the number of bootstrap replicates for SH-aLRT where 1000 is the minimum number recommended.
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	805
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	806 IQ-TREE also supports other tests such as the aBayes test (Anisimova et al., 2011) and the local bootstrap test (Adachi and Hasegawa, 1996).
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	807
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	808 You can also perform both SH-aLRT and the ultrafast bootstrap within one single run:
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	809
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	810 ::
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	811
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	812 iqtree -s example.phy -m TIM2+I+G -alrt 1000 -bb 1000
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	813
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	814 The branches of the resulting .treefile will be assigned with both SH-aLRT and UFBoot support values, which are readable by any tree viewer program like FigTree, Dendroscope or ETE. You can also look at the textual tree figure in .iqtree file:
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	815
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	816 NOTE: Tree is UNROOTED although outgroup taxon 'LngfishAu' is drawn at root
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	817 Numbers in parentheses are SH-aLRT support (%) / ultrafast bootstrap support (%)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	818
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	819 ::
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	820
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	821 +-------------LngfishAu
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	822 \|
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	823 \| +--------------LngfishSA
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	824 +-------\| (100/100)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	825 \| +------------LngfishAf
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	826 \|
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	827 \| +--------------------Frog
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	828 +------\| (99.8/100)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	829 \| +-----------------Turtle
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	830 \| +--\| (85/72)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	831 \| \| \| +------------------------Crocodile
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	832 \| \| +----\| (96.5/97)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	833 \| \| +------------------Bird
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	834 \| +--\| (39/51)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	835 \| \| +---------------------------Sphenodon
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	836 \| +-----\| (98.2/99)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	837 \| \| +-------------------------------Lizard
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	838 +---------\| (100/100)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	839 \| +--------------Human
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	840 \| +--\| (92.3/93)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	841 \| \| \| +------Seal
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	842 \| \| +--\| (68.3/75)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	843 \| \| \| +-----Cow
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	844 \| \| +--\| (99.7/100)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	845 \| \| +-------Whale
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	846 \| +----\| (99.1/100)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	847 \| \| \| +---Mouse
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	848 \| \| +---------\| (100/100)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	849 \| \| +------Rat
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	850 +-----------\| (100/100)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	851 \| +--------------Platypus
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	852 +--\| (93/98)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	853 +-----------Opossum
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	854
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	855
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	856 From this figure, the branching patterns within reptiles are poorly supported (e.g. Sphenodon with SH-aLRT: 39%, UFBoot: 51% and Turtle with SH-aLRT: 85%, UFBoot: 72%) as well as the phylogenetic position of Seal within mammals (SH-aLRT: 68.3%, UFBoot: 75%). Other branches appear to be well supported.
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	857 </help>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	858 <citations>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	859 <citation type="doi">10.1093/molbev/msu300</citation>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	860 <citation type="doi">10.1093/molbev/mst024</citation>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	861 </citations>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997 iuc parents: diff changeset	862 </tool>

Mercurial > repos > iuc > iqtree

annotate iqtree.xml @ 0:72ef801e8d98 draft