Mercurial > repos > florianbegusch > qiime2_suite

comparison qiime2/qiime_phylogeny_iqtree-ultrafast-bootstrap.xml @ 14:a0a8d77a991c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
children
comparison
equal deleted inserted replaced
13:887cd4ad8e16 14:a0a8d77a991c
1 <?xml version="1.0" ?> 1 <?xml version="1.0" ?>
2 <tool id="qiime_phylogeny_iqtree-ultrafast-bootstrap" name="qiime phylogeny iqtree-ultrafast-bootstrap" version="2019.7"> 2 <tool id="qiime_phylogeny_iqtree-ultrafast-bootstrap" name="qiime phylogeny iqtree-ultrafast-bootstrap"
3 <description> - Construct a phylogenetic tree with IQ-TREE with bootstrap supports.</description> 3 version="2020.8">
4 <requirements> 4 <description>Construct a phylogenetic tree with IQ-TREE with bootstrap supports.</description>
5 <requirement type="package" version="2019.7">qiime2</requirement> 5 <requirements>
6 </requirements> 6 <requirement type="package" version="2020.8">qiime2</requirement>
7 <command><![CDATA[ 7 </requirements>
8 <command><![CDATA[
8 qiime phylogeny iqtree-ultrafast-bootstrap 9 qiime phylogeny iqtree-ultrafast-bootstrap
9 10
10 --i-alignment=$ialignment 11 --i-alignment=$ialignment
11 12
12 #if str($pseed): 13 #if str($pseed):
13 --p-seed="$pseed" 14 --p-seed=$pseed
14 #end if 15 #end if
15 16 #if str($pncores) != 'None':
16
17 #set $pncores = '${GALAXY_SLOTS:-4}'
18 #if str($pncores):
19 --p-n-cores=$pncores 17 --p-n-cores=$pncores
20 #end if 18 #end if
21 19
22 20 #set $pncoresmax = '${GALAXY_SLOTS:-4}'
23 #if str($pnruns): 21
24 --p-n-runs=$pnruns 22 #if str($pncoresmax):
25 #end if 23 --p-n-cores-max=$pncoresmax
24 #end if
25
26 --p-n-runs=$pnruns
26 27
27 #if str($psubstitutionmodel) != 'None': 28 #if str($psubstitutionmodel) != 'None':
28 --p-substitution-model=$psubstitutionmodel 29 --p-substitution-model=$psubstitutionmodel
29 #end if 30 #end if
30 31
31 #if str($pbootstrapreplicates): 32 --p-bootstrap-replicates=$pbootstrapreplicates
32 --p-bootstrap-replicates=$pbootstrapreplicates
33 #end if
34 33
35 #if str($pninitparstrees): 34 #if str($pninitparstrees):
36 --p-n-init-pars-trees="$pninitparstrees" 35 --p-n-init-pars-trees=$pninitparstrees
37 #end if 36 #end if
38
39 #if str($pntopinittrees): 37 #if str($pntopinittrees):
40 --p-n-top-init-trees="$pntopinittrees" 38 --p-n-top-init-trees=$pntopinittrees
41 #end if 39 #end if
42
43 #if str($pnbestretaintrees): 40 #if str($pnbestretaintrees):
44 --p-n-best-retain-trees="$pnbestretaintrees" 41 --p-n-best-retain-trees=$pnbestretaintrees
45 #end if 42 #end if
46
47 #if str($pstopiter): 43 #if str($pstopiter):
48 --p-stop-iter="$pstopiter" 44 --p-stop-iter=$pstopiter
49 #end if 45 #end if
50
51 #if str($pperturbnnistrength): 46 #if str($pperturbnnistrength):
52 --p-perturb-nni-strength="$pperturbnnistrength" 47 --p-perturb-nni-strength=$pperturbnnistrength
53 #end if 48 #end if
54
55 #if str($psprradius): 49 #if str($psprradius):
56 --p-spr-radius="$psprradius" 50 --p-spr-radius=$psprradius
57 #end if 51 #end if
58
59 #if str($pnmaxufbootiter): 52 #if str($pnmaxufbootiter):
60 --p-n-max-ufboot-iter="$pnmaxufbootiter" 53 --p-n-max-ufboot-iter=$pnmaxufbootiter
61 #end if 54 #end if
62
63 #if str($pnufbootsteps): 55 #if str($pnufbootsteps):
64 --p-n-ufboot-steps="$pnufbootsteps" 56 --p-n-ufboot-steps=$pnufbootsteps
65 #end if 57 #end if
66
67 #if str($pmincorufboot): 58 #if str($pmincorufboot):
68 --p-min-cor-ufboot="$pmincorufboot" 59 --p-min-cor-ufboot=$pmincorufboot
69 #end if 60 #end if
70
71 #if str($pepbreakufboot): 61 #if str($pepbreakufboot):
72 --p-ep-break-ufboot="$pepbreakufboot" 62 --p-ep-break-ufboot=$pepbreakufboot
73 #end if 63 #end if
74
75 #if $pallnni: 64 #if $pallnni:
76 --p-allnni 65 --p-allnni
77 #end if 66 #end if
78 67
79 #if str($palrt): 68 #if str($palrt):
80 --p-alrt="$palrt" 69 --p-alrt=$palrt
81 #end if 70 #end if
82
83 #if $pabayes: 71 #if $pabayes:
84 --p-abayes 72 --p-abayes
85 #end if 73 #end if
86 74
87 #if str($plbp): 75 #if str($plbp):
88 --p-lbp="$plbp" 76 --p-lbp=$plbp
89 #end if 77 #end if
90
91 #if $pbnni: 78 #if $pbnni:
92 --p-bnni 79 --p-bnni
93 #end if 80 #end if
94 81
95 #if $psafe: 82 #if $psafe:
96 --p-safe 83 --p-safe
97 #end if 84 #end if
98 85
99 --o-tree=otree 86 --o-tree=otree
87
88 #if str($examples) != 'None':
89 --examples=$examples
90 #end if
91
100 ; 92 ;
101 cp otree.qza $otree 93 cp otree.qza $otree
102 ]]></command> 94
103 <inputs> 95 ]]></command>
104 <param format="qza,no_unzip.zip" label="--i-alignment: ARTIFACT FeatureData[AlignedSequence] Aligned sequences to be used for phylogenetic reconstruction. [required]" name="ialignment" optional="False" type="data"/> 96 <inputs>
105 <param label="--p-seed: INTEGER Random number seed. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pseed" optional="True" type="integer"/> 97 <param format="qza,no_unzip.zip" label="--i-alignment: ARTIFACT FeatureData[AlignedSequence] Aligned sequences to be used for phylogenetic reconstruction. [required]" name="ialignment" optional="False" type="data" />
106 <param label="--p-n-runs: INTEGER Number of indepedent runs. Multiple independent Range(1, None) runs (e.g. 10) can outperform a single run in terms of likelihood maximisation. [default: 1]" name="pnruns" optional="True" type="integer" min="1" value="1"/> 98 <param label="--p-seed: INTEGER Random number seed. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pseed" optional="False" type="text" />
107 <param label="--p-substitution-model: " name="psubstitutionmodel" optional="True" type="select"> 99 <param label="--p-n-cores: " name="pncores" optional="True" type="select">
108 <option selected="True" value="None">Selection is Optional</option> 100 <option selected="True" value="None">Selection is Optional</option>
109 <option value="JC">JC</option> 101 <option value="Int % Range(1">Int % Range(1</option>
110 <option value="JC+I">JC+I</option> 102 <option value="None">None</option>
111 <option value="JC+G">JC+G</option> 103 </param>
112 <option value="JC+I+G">JC+I+G</option> 104 <param label="--p-n-runs: INTEGER Number of indepedent runs. Multiple independent Range(1, None) runs (e.g. 10) can outperform a single run in terms of likelihood maximisation. [default: 1]" min="1" name="pnruns" optional="True" type="integer" value="1" />
113 <option value="JC+R2">JC+R2</option> 105 <param label="--p-substitution-model: " name="psubstitutionmodel" optional="True" type="select">
114 <option value="JC+R3">JC+R3</option> 106 <option selected="True" value="None">Selection is Optional</option>
115 <option value="JC+R4">JC+R4</option> 107 <option value="JC">JC</option>
116 <option value="JC+R5">JC+R5</option> 108 <option value="JC+I">JC+I</option>
117 <option value="JC+R6">JC+R6</option> 109 <option value="JC+G">JC+G</option>
118 <option value="JC+R7">JC+R7</option> 110 <option value="JC+I+G">JC+I+G</option>
119 <option value="JC+R8">JC+R8</option> 111 <option value="JC+R2">JC+R2</option>
120 <option value="JC+R9">JC+R9</option> 112 <option value="JC+R3">JC+R3</option>
121 <option value="JC+R10">JC+R10</option> 113 <option value="JC+R4">JC+R4</option>
122 <option value="F81">F81</option> 114 <option value="JC+R5">JC+R5</option>
123 <option value="F81+I">F81+I</option> 115 <option value="JC+R6">JC+R6</option>
124 <option value="F81+G">F81+G</option> 116 <option value="JC+R7">JC+R7</option>
125 <option value="F81+I+G">F81+I+G</option> 117 <option value="JC+R8">JC+R8</option>
126 <option value="F81+R2">F81+R2</option> 118 <option value="JC+R9">JC+R9</option>
127 <option value="F81+R3">F81+R3</option> 119 <option value="JC+R10">JC+R10</option>
128 <option value="F81+R4">F81+R4</option> 120 <option value="F81">F81</option>
129 <option value="F81+R5">F81+R5</option> 121 <option value="F81+I">F81+I</option>
130 <option value="F81+R6">F81+R6</option> 122 <option value="F81+G">F81+G</option>
131 <option value="F81+R7">F81+R7</option> 123 <option value="F81+I+G">F81+I+G</option>
132 <option value="F81+R8">F81+R8</option> 124 <option value="F81+R2">F81+R2</option>
133 <option value="F81+R9">F81+R9</option> 125 <option value="F81+R3">F81+R3</option>
134 <option value="F81+R10">F81+R10</option> 126 <option value="F81+R4">F81+R4</option>
135 <option value="K80">K80</option> 127 <option value="F81+R5">F81+R5</option>
136 <option value="K80+I">K80+I</option> 128 <option value="F81+R6">F81+R6</option>
137 <option value="K80+G">K80+G</option> 129 <option value="F81+R7">F81+R7</option>
138 <option value="K80+I+G">K80+I+G</option> 130 <option value="F81+R8">F81+R8</option>
139 <option value="K80+R2">K80+R2</option> 131 <option value="F81+R9">F81+R9</option>
140 <option value="K80+R3">K80+R3</option> 132 <option value="F81+R10">F81+R10</option>
141 <option value="K80+R4">K80+R4</option> 133 <option value="K80">K80</option>
142 <option value="K80+R5">K80+R5</option> 134 <option value="K80+I">K80+I</option>
143 <option value="K80+R6">K80+R6</option> 135 <option value="K80+G">K80+G</option>
144 <option value="K80+R7">K80+R7</option> 136 <option value="K80+I+G">K80+I+G</option>
145 <option value="K80+R8">K80+R8</option> 137 <option value="K80+R2">K80+R2</option>
146 <option value="K80+R9">K80+R9</option> 138 <option value="K80+R3">K80+R3</option>
147 <option value="K80+R10">K80+R10</option> 139 <option value="K80+R4">K80+R4</option>
148 <option value="HKY">HKY</option> 140 <option value="K80+R5">K80+R5</option>
149 <option value="HKY+I">HKY+I</option> 141 <option value="K80+R6">K80+R6</option>
150 <option value="HKY+G">HKY+G</option> 142 <option value="K80+R7">K80+R7</option>
151 <option value="HKY+I+G">HKY+I+G</option> 143 <option value="K80+R8">K80+R8</option>
152 <option value="HKY+R2">HKY+R2</option> 144 <option value="K80+R9">K80+R9</option>
153 <option value="HKY+R3">HKY+R3</option> 145 <option value="K80+R10">K80+R10</option>
154 <option value="HKY+R4">HKY+R4</option> 146 <option value="HKY">HKY</option>
155 <option value="HKY+R5">HKY+R5</option> 147 <option value="HKY+I">HKY+I</option>
156 <option value="HKY+R6">HKY+R6</option> 148 <option value="HKY+G">HKY+G</option>
157 <option value="HKY+R7">HKY+R7</option> 149 <option value="HKY+I+G">HKY+I+G</option>
158 <option value="HKY+R8">HKY+R8</option> 150 <option value="HKY+R2">HKY+R2</option>
159 <option value="HKY+R9">HKY+R9</option> 151 <option value="HKY+R3">HKY+R3</option>
160 <option value="HKY+R10">HKY+R10</option> 152 <option value="HKY+R4">HKY+R4</option>
161 <option value="TNe">TNe</option> 153 <option value="HKY+R5">HKY+R5</option>
162 <option value="TNe+I">TNe+I</option> 154 <option value="HKY+R6">HKY+R6</option>
163 <option value="TNe+G">TNe+G</option> 155 <option value="HKY+R7">HKY+R7</option>
164 <option value="TNe+I+G">TNe+I+G</option> 156 <option value="HKY+R8">HKY+R8</option>
165 <option value="TNe+R2">TNe+R2</option> 157 <option value="HKY+R9">HKY+R9</option>
166 <option value="TNe+R3">TNe+R3</option> 158 <option value="HKY+R10">HKY+R10</option>
167 <option value="TNe+R4">TNe+R4</option> 159 <option value="TNe">TNe</option>
168 <option value="TNe+R5">TNe+R5</option> 160 <option value="TNe+I">TNe+I</option>
169 <option value="TNe+R6">TNe+R6</option> 161 <option value="TNe+G">TNe+G</option>
170 <option value="TNe+R7">TNe+R7</option> 162 <option value="TNe+I+G">TNe+I+G</option>
171 <option value="TNe+R8">TNe+R8</option> 163 <option value="TNe+R2">TNe+R2</option>
172 <option value="TNe+R9">TNe+R9</option> 164 <option value="TNe+R3">TNe+R3</option>
173 <option value="TNe+R10">TNe+R10</option> 165 <option value="TNe+R4">TNe+R4</option>
174 <option value="TN">TN</option> 166 <option value="TNe+R5">TNe+R5</option>
175 <option value="TN+I">TN+I</option> 167 <option value="TNe+R6">TNe+R6</option>
176 <option value="TN+G">TN+G</option> 168 <option value="TNe+R7">TNe+R7</option>
177 <option value="TN+I+G">TN+I+G</option> 169 <option value="TNe+R8">TNe+R8</option>
178 <option value="TN+R2">TN+R2</option> 170 <option value="TNe+R9">TNe+R9</option>
179 <option value="TN+R3">TN+R3</option> 171 <option value="TNe+R10">TNe+R10</option>
180 <option value="TN+R4">TN+R4</option> 172 <option value="TN">TN</option>
181 <option value="TN+R5">TN+R5</option> 173 <option value="TN+I">TN+I</option>
182 <option value="TN+R6">TN+R6</option> 174 <option value="TN+G">TN+G</option>
183 <option value="TN+R7">TN+R7</option> 175 <option value="TN+I+G">TN+I+G</option>
184 <option value="TN+R8">TN+R8</option> 176 <option value="TN+R2">TN+R2</option>
185 <option value="TN+R9">TN+R9</option> 177 <option value="TN+R3">TN+R3</option>
186 <option value="TN+R10">TN+R10</option> 178 <option value="TN+R4">TN+R4</option>
187 <option value="K81">K81</option> 179 <option value="TN+R5">TN+R5</option>
188 <option value="K81+I">K81+I</option> 180 <option value="TN+R6">TN+R6</option>
189 <option value="K81+G">K81+G</option> 181 <option value="TN+R7">TN+R7</option>
190 <option value="K81+I+G">K81+I+G</option> 182 <option value="TN+R8">TN+R8</option>
191 <option value="K81+R2">K81+R2</option> 183 <option value="TN+R9">TN+R9</option>
192 <option value="K81+R3">K81+R3</option> 184 <option value="TN+R10">TN+R10</option>
193 <option value="K81+R4">K81+R4</option> 185 <option value="K81">K81</option>
194 <option value="K81+R5">K81+R5</option> 186 <option value="K81+I">K81+I</option>
195 <option value="K81+R6">K81+R6</option> 187 <option value="K81+G">K81+G</option>
196 <option value="K81+R7">K81+R7</option> 188 <option value="K81+I+G">K81+I+G</option>
197 <option value="K81+R8">K81+R8</option> 189 <option value="K81+R2">K81+R2</option>
198 <option value="K81+R9">K81+R9</option> 190 <option value="K81+R3">K81+R3</option>
199 <option value="K81+R10">K81+R10</option> 191 <option value="K81+R4">K81+R4</option>
200 <option value="K81u">K81u</option> 192 <option value="K81+R5">K81+R5</option>
201 <option value="K81u+I">K81u+I</option> 193 <option value="K81+R6">K81+R6</option>
202 <option value="K81u+G">K81u+G</option> 194 <option value="K81+R7">K81+R7</option>
203 <option value="K81u+I+G">K81u+I+G</option> 195 <option value="K81+R8">K81+R8</option>
204 <option value="K81u+R2">K81u+R2</option> 196 <option value="K81+R9">K81+R9</option>
205 <option value="K81u+R3">K81u+R3</option> 197 <option value="K81+R10">K81+R10</option>
206 <option value="K81u+R4">K81u+R4</option> 198 <option value="K81u">K81u</option>
207 <option value="K81u+R5">K81u+R5</option> 199 <option value="K81u+I">K81u+I</option>
208 <option value="K81u+R6">K81u+R6</option> 200 <option value="K81u+G">K81u+G</option>
209 <option value="K81u+R7">K81u+R7</option> 201 <option value="K81u+I+G">K81u+I+G</option>
210 <option value="K81u+R8">K81u+R8</option> 202 <option value="K81u+R2">K81u+R2</option>
211 <option value="K81u+R9">K81u+R9</option> 203 <option value="K81u+R3">K81u+R3</option>
212 <option value="K81u+R10">K81u+R10</option> 204 <option value="K81u+R4">K81u+R4</option>
213 <option value="TPM2">TPM2</option> 205 <option value="K81u+R5">K81u+R5</option>
214 <option value="TPM2+I">TPM2+I</option> 206 <option value="K81u+R6">K81u+R6</option>
215 <option value="TPM2+G">TPM2+G</option> 207 <option value="K81u+R7">K81u+R7</option>
216 <option value="TPM2+I+G">TPM2+I+G</option> 208 <option value="K81u+R8">K81u+R8</option>
217 <option value="TPM2+R2">TPM2+R2</option> 209 <option value="K81u+R9">K81u+R9</option>
218 <option value="TPM2+R3">TPM2+R3</option> 210 <option value="K81u+R10">K81u+R10</option>
219 <option value="TPM2+R4">TPM2+R4</option> 211 <option value="TPM2">TPM2</option>
220 <option value="TPM2+R5">TPM2+R5</option> 212 <option value="TPM2+I">TPM2+I</option>
221 <option value="TPM2+R6">TPM2+R6</option> 213 <option value="TPM2+G">TPM2+G</option>
222 <option value="TPM2+R7">TPM2+R7</option> 214 <option value="TPM2+I+G">TPM2+I+G</option>
223 <option value="TPM2+R8">TPM2+R8</option> 215 <option value="TPM2+R2">TPM2+R2</option>
224 <option value="TPM2+R9">TPM2+R9</option> 216 <option value="TPM2+R3">TPM2+R3</option>
225 <option value="TPM2+R10">TPM2+R10</option> 217 <option value="TPM2+R4">TPM2+R4</option>
226 <option value="TPM2u">TPM2u</option> 218 <option value="TPM2+R5">TPM2+R5</option>
227 <option value="TPM2u+I">TPM2u+I</option> 219 <option value="TPM2+R6">TPM2+R6</option>
228 <option value="TPM2u+G">TPM2u+G</option> 220 <option value="TPM2+R7">TPM2+R7</option>
229 <option value="TPM2u+I+G">TPM2u+I+G</option> 221 <option value="TPM2+R8">TPM2+R8</option>
230 <option value="TPM2u+R2">TPM2u+R2</option> 222 <option value="TPM2+R9">TPM2+R9</option>
231 <option value="TPM2u+R3">TPM2u+R3</option> 223 <option value="TPM2+R10">TPM2+R10</option>
232 <option value="TPM2u+R4">TPM2u+R4</option> 224 <option value="TPM2u">TPM2u</option>
233 <option value="TPM2u+R5">TPM2u+R5</option> 225 <option value="TPM2u+I">TPM2u+I</option>
234 <option value="TPM2u+R6">TPM2u+R6</option> 226 <option value="TPM2u+G">TPM2u+G</option>
235 <option value="TPM2u+R7">TPM2u+R7</option> 227 <option value="TPM2u+I+G">TPM2u+I+G</option>
236 <option value="TPM2u+R8">TPM2u+R8</option> 228 <option value="TPM2u+R2">TPM2u+R2</option>
237 <option value="TPM2u+R9">TPM2u+R9</option> 229 <option value="TPM2u+R3">TPM2u+R3</option>
238 <option value="TPM2u+R10">TPM2u+R10</option> 230 <option value="TPM2u+R4">TPM2u+R4</option>
239 <option value="TPM3">TPM3</option> 231 <option value="TPM2u+R5">TPM2u+R5</option>
240 <option value="TPM3+I">TPM3+I</option> 232 <option value="TPM2u+R6">TPM2u+R6</option>
241 <option value="TPM3+G">TPM3+G</option> 233 <option value="TPM2u+R7">TPM2u+R7</option>
242 <option value="TPM3+I+G">TPM3+I+G</option> 234 <option value="TPM2u+R8">TPM2u+R8</option>
243 <option value="TPM3+R2">TPM3+R2</option> 235 <option value="TPM2u+R9">TPM2u+R9</option>
244 <option value="TPM3+R3">TPM3+R3</option> 236 <option value="TPM2u+R10">TPM2u+R10</option>
245 <option value="TPM3+R4">TPM3+R4</option> 237 <option value="TPM3">TPM3</option>
246 <option value="TPM3+R5">TPM3+R5</option> 238 <option value="TPM3+I">TPM3+I</option>
247 <option value="TPM3+R6">TPM3+R6</option> 239 <option value="TPM3+G">TPM3+G</option>
248 <option value="TPM3+R7">TPM3+R7</option> 240 <option value="TPM3+I+G">TPM3+I+G</option>
249 <option value="TPM3+R8">TPM3+R8</option> 241 <option value="TPM3+R2">TPM3+R2</option>
250 <option value="TPM3+R9">TPM3+R9</option> 242 <option value="TPM3+R3">TPM3+R3</option>
251 <option value="TPM3+R10">TPM3+R10</option> 243 <option value="TPM3+R4">TPM3+R4</option>
252 <option value="TPM3u">TPM3u</option> 244 <option value="TPM3+R5">TPM3+R5</option>
253 <option value="TPM3u+I">TPM3u+I</option> 245 <option value="TPM3+R6">TPM3+R6</option>
254 <option value="TPM3u+G">TPM3u+G</option> 246 <option value="TPM3+R7">TPM3+R7</option>
255 <option value="TPM3u+I+G">TPM3u+I+G</option> 247 <option value="TPM3+R8">TPM3+R8</option>
256 <option value="TPM3u+R2">TPM3u+R2</option> 248 <option value="TPM3+R9">TPM3+R9</option>
257 <option value="TPM3u+R3">TPM3u+R3</option> 249 <option value="TPM3+R10">TPM3+R10</option>
258 <option value="TPM3u+R4">TPM3u+R4</option> 250 <option value="TPM3u">TPM3u</option>
259 <option value="TPM3u+R5">TPM3u+R5</option> 251 <option value="TPM3u+I">TPM3u+I</option>
260 <option value="TPM3u+R6">TPM3u+R6</option> 252 <option value="TPM3u+G">TPM3u+G</option>
261 <option value="TPM3u+R7">TPM3u+R7</option> 253 <option value="TPM3u+I+G">TPM3u+I+G</option>
262 <option value="TPM3u+R8">TPM3u+R8</option> 254 <option value="TPM3u+R2">TPM3u+R2</option>
263 <option value="TPM3u+R9">TPM3u+R9</option> 255 <option value="TPM3u+R3">TPM3u+R3</option>
264 <option value="TPM3u+R10">TPM3u+R10</option> 256 <option value="TPM3u+R4">TPM3u+R4</option>
265 <option value="TIMe">TIMe</option> 257 <option value="TPM3u+R5">TPM3u+R5</option>
266 <option value="TIMe+I">TIMe+I</option> 258 <option value="TPM3u+R6">TPM3u+R6</option>
267 <option value="TIMe+G">TIMe+G</option> 259 <option value="TPM3u+R7">TPM3u+R7</option>
268 <option value="TIMe+I+G">TIMe+I+G</option> 260 <option value="TPM3u+R8">TPM3u+R8</option>
269 <option value="TIMe+R2">TIMe+R2</option> 261 <option value="TPM3u+R9">TPM3u+R9</option>
270 <option value="TIMe+R3">TIMe+R3</option> 262 <option value="TPM3u+R10">TPM3u+R10</option>
271 <option value="TIMe+R4">TIMe+R4</option> 263 <option value="TIMe">TIMe</option>
272 <option value="TIMe+R5">TIMe+R5</option> 264 <option value="TIMe+I">TIMe+I</option>
273 <option value="TIMe+R6">TIMe+R6</option> 265 <option value="TIMe+G">TIMe+G</option>
274 <option value="TIMe+R7">TIMe+R7</option> 266 <option value="TIMe+I+G">TIMe+I+G</option>
275 <option value="TIMe+R8">TIMe+R8</option> 267 <option value="TIMe+R2">TIMe+R2</option>
276 <option value="TIMe+R9">TIMe+R9</option> 268 <option value="TIMe+R3">TIMe+R3</option>
277 <option value="TIMe+R10">TIMe+R10</option> 269 <option value="TIMe+R4">TIMe+R4</option>
278 <option value="TIM">TIM</option> 270 <option value="TIMe+R5">TIMe+R5</option>
279 <option value="TIM+I">TIM+I</option> 271 <option value="TIMe+R6">TIMe+R6</option>
280 <option value="TIM+G">TIM+G</option> 272 <option value="TIMe+R7">TIMe+R7</option>
281 <option value="TIM+I+G">TIM+I+G</option> 273 <option value="TIMe+R8">TIMe+R8</option>
282 <option value="TIM+R2">TIM+R2</option> 274 <option value="TIMe+R9">TIMe+R9</option>
283 <option value="TIM+R3">TIM+R3</option> 275 <option value="TIMe+R10">TIMe+R10</option>
284 <option value="TIM+R4">TIM+R4</option> 276 <option value="TIM">TIM</option>
285 <option value="TIM+R5">TIM+R5</option> 277 <option value="TIM+I">TIM+I</option>
286 <option value="TIM+R6">TIM+R6</option> 278 <option value="TIM+G">TIM+G</option>
287 <option value="TIM+R7">TIM+R7</option> 279 <option value="TIM+I+G">TIM+I+G</option>
288 <option value="TIM+R8">TIM+R8</option> 280 <option value="TIM+R2">TIM+R2</option>
289 <option value="TIM+R9">TIM+R9</option> 281 <option value="TIM+R3">TIM+R3</option>
290 <option value="TIM+R10">TIM+R10</option> 282 <option value="TIM+R4">TIM+R4</option>
291 <option value="TIM2e">TIM2e</option> 283 <option value="TIM+R5">TIM+R5</option>
292 <option value="TIM2e+I">TIM2e+I</option> 284 <option value="TIM+R6">TIM+R6</option>
293 <option value="TIM2e+G">TIM2e+G</option> 285 <option value="TIM+R7">TIM+R7</option>
294 <option value="TIM2e+I+G">TIM2e+I+G</option> 286 <option value="TIM+R8">TIM+R8</option>
295 <option value="TIM2e+R2">TIM2e+R2</option> 287 <option value="TIM+R9">TIM+R9</option>
296 <option value="TIM2e+R3">TIM2e+R3</option> 288 <option value="TIM+R10">TIM+R10</option>
297 <option value="TIM2e+R4">TIM2e+R4</option> 289 <option value="TIM2e">TIM2e</option>
298 <option value="TIM2e+R5">TIM2e+R5</option> 290 <option value="TIM2e+I">TIM2e+I</option>
299 <option value="TIM2e+R6">TIM2e+R6</option> 291 <option value="TIM2e+G">TIM2e+G</option>
300 <option value="TIM2e+R7">TIM2e+R7</option> 292 <option value="TIM2e+I+G">TIM2e+I+G</option>
301 <option value="TIM2e+R8">TIM2e+R8</option> 293 <option value="TIM2e+R2">TIM2e+R2</option>
302 <option value="TIM2e+R9">TIM2e+R9</option> 294 <option value="TIM2e+R3">TIM2e+R3</option>
303 <option value="TIM2e+R10">TIM2e+R10</option> 295 <option value="TIM2e+R4">TIM2e+R4</option>
304 <option value="TIM2">TIM2</option> 296 <option value="TIM2e+R5">TIM2e+R5</option>
305 <option value="TIM2+I">TIM2+I</option> 297 <option value="TIM2e+R6">TIM2e+R6</option>
306 <option value="TIM2+G">TIM2+G</option> 298 <option value="TIM2e+R7">TIM2e+R7</option>
307 <option value="TIM2+I+G">TIM2+I+G</option> 299 <option value="TIM2e+R8">TIM2e+R8</option>
308 <option value="TIM2+R2">TIM2+R2</option> 300 <option value="TIM2e+R9">TIM2e+R9</option>
309 <option value="TIM2+R3">TIM2+R3</option> 301 <option value="TIM2e+R10">TIM2e+R10</option>
310 <option value="TIM2+R4">TIM2+R4</option> 302 <option value="TIM2">TIM2</option>
311 <option value="TIM2+R5">TIM2+R5</option> 303 <option value="TIM2+I">TIM2+I</option>
312 <option value="TIM2+R6">TIM2+R6</option> 304 <option value="TIM2+G">TIM2+G</option>
313 <option value="TIM2+R7">TIM2+R7</option> 305 <option value="TIM2+I+G">TIM2+I+G</option>
314 <option value="TIM2+R8">TIM2+R8</option> 306 <option value="TIM2+R2">TIM2+R2</option>
315 <option value="TIM2+R9">TIM2+R9</option> 307 <option value="TIM2+R3">TIM2+R3</option>
316 <option value="TIM2+R10">TIM2+R10</option> 308 <option value="TIM2+R4">TIM2+R4</option>
317 <option value="TIM3e">TIM3e</option> 309 <option value="TIM2+R5">TIM2+R5</option>
318 <option value="TIM3e+I">TIM3e+I</option> 310 <option value="TIM2+R6">TIM2+R6</option>
319 <option value="TIM3e+G">TIM3e+G</option> 311 <option value="TIM2+R7">TIM2+R7</option>
320 <option value="TIM3e+I+G">TIM3e+I+G</option> 312 <option value="TIM2+R8">TIM2+R8</option>
321 <option value="TIM3e+R2">TIM3e+R2</option> 313 <option value="TIM2+R9">TIM2+R9</option>
322 <option value="TIM3e+R3">TIM3e+R3</option> 314 <option value="TIM2+R10">TIM2+R10</option>
323 <option value="TIM3e+R4">TIM3e+R4</option> 315 <option value="TIM3e">TIM3e</option>
324 <option value="TIM3e+R5">TIM3e+R5</option> 316 <option value="TIM3e+I">TIM3e+I</option>
325 <option value="TIM3e+R6">TIM3e+R6</option> 317 <option value="TIM3e+G">TIM3e+G</option>
326 <option value="TIM3e+R7">TIM3e+R7</option> 318 <option value="TIM3e+I+G">TIM3e+I+G</option>
327 <option value="TIM3e+R8">TIM3e+R8</option> 319 <option value="TIM3e+R2">TIM3e+R2</option>
328 <option value="TIM3e+R9">TIM3e+R9</option> 320 <option value="TIM3e+R3">TIM3e+R3</option>
329 <option value="TIM3e+R10">TIM3e+R10</option> 321 <option value="TIM3e+R4">TIM3e+R4</option>
330 <option value="TIM3">TIM3</option> 322 <option value="TIM3e+R5">TIM3e+R5</option>
331 <option value="TIM3+I">TIM3+I</option> 323 <option value="TIM3e+R6">TIM3e+R6</option>
332 <option value="TIM3+G">TIM3+G</option> 324 <option value="TIM3e+R7">TIM3e+R7</option>
333 <option value="TIM3+I+G">TIM3+I+G</option> 325 <option value="TIM3e+R8">TIM3e+R8</option>
334 <option value="TIM3+R2">TIM3+R2</option> 326 <option value="TIM3e+R9">TIM3e+R9</option>
335 <option value="TIM3+R3">TIM3+R3</option> 327 <option value="TIM3e+R10">TIM3e+R10</option>
336 <option value="TIM3+R4">TIM3+R4</option> 328 <option value="TIM3">TIM3</option>
337 <option value="TIM3+R5">TIM3+R5</option> 329 <option value="TIM3+I">TIM3+I</option>
338 <option value="TIM3+R6">TIM3+R6</option> 330 <option value="TIM3+G">TIM3+G</option>
339 <option value="TIM3+R7">TIM3+R7</option> 331 <option value="TIM3+I+G">TIM3+I+G</option>
340 <option value="TIM3+R8">TIM3+R8</option> 332 <option value="TIM3+R2">TIM3+R2</option>
341 <option value="TIM3+R9">TIM3+R9</option> 333 <option value="TIM3+R3">TIM3+R3</option>
342 <option value="TIM3+R10">TIM3+R10</option> 334 <option value="TIM3+R4">TIM3+R4</option>
343 <option value="TVMe">TVMe</option> 335 <option value="TIM3+R5">TIM3+R5</option>
344 <option value="TVMe+I">TVMe+I</option> 336 <option value="TIM3+R6">TIM3+R6</option>
345 <option value="TVMe+G">TVMe+G</option> 337 <option value="TIM3+R7">TIM3+R7</option>
346 <option value="TVMe+I+G">TVMe+I+G</option> 338 <option value="TIM3+R8">TIM3+R8</option>
347 <option value="TVMe+R2">TVMe+R2</option> 339 <option value="TIM3+R9">TIM3+R9</option>
348 <option value="TVMe+R3">TVMe+R3</option> 340 <option value="TIM3+R10">TIM3+R10</option>
349 <option value="TVMe+R4">TVMe+R4</option> 341 <option value="TVMe">TVMe</option>
350 <option value="TVMe+R5">TVMe+R5</option> 342 <option value="TVMe+I">TVMe+I</option>
351 <option value="TVMe+R6">TVMe+R6</option> 343 <option value="TVMe+G">TVMe+G</option>
352 <option value="TVMe+R7">TVMe+R7</option> 344 <option value="TVMe+I+G">TVMe+I+G</option>
353 <option value="TVMe+R8">TVMe+R8</option> 345 <option value="TVMe+R2">TVMe+R2</option>
354 <option value="TVMe+R9">TVMe+R9</option> 346 <option value="TVMe+R3">TVMe+R3</option>
355 <option value="TVMe+R10">TVMe+R10</option> 347 <option value="TVMe+R4">TVMe+R4</option>
356 <option value="TVM">TVM</option> 348 <option value="TVMe+R5">TVMe+R5</option>
357 <option value="TVM+I">TVM+I</option> 349 <option value="TVMe+R6">TVMe+R6</option>
358 <option value="TVM+G">TVM+G</option> 350 <option value="TVMe+R7">TVMe+R7</option>
359 <option value="TVM+I+G">TVM+I+G</option> 351 <option value="TVMe+R8">TVMe+R8</option>
360 <option value="TVM+R2">TVM+R2</option> 352 <option value="TVMe+R9">TVMe+R9</option>
361 <option value="TVM+R3">TVM+R3</option> 353 <option value="TVMe+R10">TVMe+R10</option>
362 <option value="TVM+R4">TVM+R4</option> 354 <option value="TVM">TVM</option>
363 <option value="TVM+R5">TVM+R5</option> 355 <option value="TVM+I">TVM+I</option>
364 <option value="TVM+R6">TVM+R6</option> 356 <option value="TVM+G">TVM+G</option>
365 <option value="TVM+R7">TVM+R7</option> 357 <option value="TVM+I+G">TVM+I+G</option>
366 <option value="TVM+R8">TVM+R8</option> 358 <option value="TVM+R2">TVM+R2</option>
367 <option value="TVM+R9">TVM+R9</option> 359 <option value="TVM+R3">TVM+R3</option>
368 <option value="TVM+R10">TVM+R10</option> 360 <option value="TVM+R4">TVM+R4</option>
369 <option value="SYM">SYM</option> 361 <option value="TVM+R5">TVM+R5</option>
370 <option value="SYM+I">SYM+I</option> 362 <option value="TVM+R6">TVM+R6</option>
371 <option value="SYM+G">SYM+G</option> 363 <option value="TVM+R7">TVM+R7</option>
372 <option value="SYM+I+G">SYM+I+G</option> 364 <option value="TVM+R8">TVM+R8</option>
373 <option value="SYM+R2">SYM+R2</option> 365 <option value="TVM+R9">TVM+R9</option>
374 <option value="SYM+R3">SYM+R3</option> 366 <option value="TVM+R10">TVM+R10</option>
375 <option value="SYM+R4">SYM+R4</option> 367 <option value="SYM">SYM</option>
376 <option value="SYM+R5">SYM+R5</option> 368 <option value="SYM+I">SYM+I</option>
377 <option value="SYM+R6">SYM+R6</option> 369 <option value="SYM+G">SYM+G</option>
378 <option value="SYM+R7">SYM+R7</option> 370 <option value="SYM+I+G">SYM+I+G</option>
379 <option value="SYM+R8">SYM+R8</option> 371 <option value="SYM+R2">SYM+R2</option>
380 <option value="SYM+R9">SYM+R9</option> 372 <option value="SYM+R3">SYM+R3</option>
381 <option value="SYM+R10">SYM+R10</option> 373 <option value="SYM+R4">SYM+R4</option>
382 <option value="GTR">GTR</option> 374 <option value="SYM+R5">SYM+R5</option>
383 <option value="GTR+I">GTR+I</option> 375 <option value="SYM+R6">SYM+R6</option>
384 <option value="GTR+G">GTR+G</option> 376 <option value="SYM+R7">SYM+R7</option>
385 <option value="GTR+I+G">GTR+I+G</option> 377 <option value="SYM+R8">SYM+R8</option>
386 <option value="GTR+R2">GTR+R2</option> 378 <option value="SYM+R9">SYM+R9</option>
387 <option value="GTR+R3">GTR+R3</option> 379 <option value="SYM+R10">SYM+R10</option>
388 <option value="GTR+R4">GTR+R4</option> 380 <option value="GTR">GTR</option>
389 <option value="GTR+R5">GTR+R5</option> 381 <option value="GTR+I">GTR+I</option>
390 <option value="GTR+R6">GTR+R6</option> 382 <option value="GTR+G">GTR+G</option>
391 <option value="GTR+R7">GTR+R7</option> 383 <option value="GTR+I+G">GTR+I+G</option>
392 <option value="GTR+R8">GTR+R8</option> 384 <option value="GTR+R2">GTR+R2</option>
393 <option value="GTR+R9">GTR+R9</option> 385 <option value="GTR+R3">GTR+R3</option>
394 <option value="GTR+R10">GTR+R10</option> 386 <option value="GTR+R4">GTR+R4</option>
395 <option value="MFP">MFP</option> 387 <option value="GTR+R5">GTR+R5</option>
396 <option value="TEST">TEST</option> 388 <option value="GTR+R6">GTR+R6</option>
397 </param> 389 <option value="GTR+R7">GTR+R7</option>
398 <param label="--p-bootstrap-replicates: INTEGER Range(1000, None) The number of bootstrap searches to perform. Minimum of 1000 recomended. [default: 1000]" name="pbootstrapreplicates" optional="True" type="integer" min="1000" value="1000"/> 390 <option value="GTR+R8">GTR+R8</option>
399 <param label="--p-n-init-pars-trees: INTEGER Range(1, None) Number of initial parsimony trees. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pninitparstrees" optional="True" type="integer" min="1"/> 391 <option value="GTR+R9">GTR+R9</option>
400 <param label="--p-n-top-init-trees: INTEGER Range(1, None) Number of top initial trees. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pntopinittrees" optional="True" type="integer" min="1"/> 392 <option value="GTR+R10">GTR+R10</option>
401 <param label="--p-n-best-retain-trees: INTEGER Range(1, None) Number of best trees retained during search. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pnbestretaintrees" optional="True" type="integer" min="1"/> 393 <option value="MFP">MFP</option>
402 <param label="--p-stop-iter: INTEGER Number of unsuccessful iterations to stop. If not Range(1, None) set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pstopiter" optional="True" type="integer" min="1"/> 394 <option value="TEST">TEST</option>
403 <param label="--p-perturb-nni-strength: NUMBER Range(0.01, 99) Perturbation strength for randomized NNI. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pperturbnnistrength" optional="True" type="float" min="0.01" max="99"/> 395 </param>
404 <param label="--p-spr-radius: INTEGER Radius for parsimony SPR search. If not set, Range(1, None) program defaults will be used. See IQ-TREE manual for details. [optional]" name="psprradius" optional="True" type="integer" min="1"/> 396 <param label="--p-bootstrap-replicates: INTEGER Range(1000, None) The number of bootstrap searches to perform. Minimum of 1000 recomended. [default: 1000]" min="1000" name="pbootstrapreplicates" optional="True" type="integer" value="1000" />
405 <param label="--p-n-max-ufboot-iter: INTEGER Range(1, None) Maximum number of iterations. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pnmaxufbootiter" optional="True" type="integer" min="1"/> 397 <param label="--p-n-init-pars-trees: INTEGER Range(1, None) Number of initial parsimony trees. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pninitparstrees" optional="False" type="text" />
406 <param label="--p-n-ufboot-steps: INTEGER Range(1, None) Number of iterations for UFBoot stopping rule. If not set, program defaults will be used.See IQ-TREE manual for details. [optional]" name="pnufbootsteps" optional="True" type="integer" min="1"/> 398 <param label="--p-n-top-init-trees: INTEGER Range(1, None) Number of top initial trees. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pntopinittrees" optional="False" type="text" />
407 <param label="--p-min-cor-ufboot: NUMBER Range(0.51, 0.99) Minimum correlation coefficient. If not set, program defaults will be used.See IQ-TREE manual for details. [optional]" name="pmincorufboot" optional="True" type="float" min="0.51" max="0.99"/> 399 <param label="--p-n-best-retain-trees: INTEGER Range(1, None) Number of best trees retained during search. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pnbestretaintrees" optional="False" type="text" />
408 <param label="--p-ep-break-ufboot: NUMBER Range(0.01, 0.99) Epsilon value to break tie. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pepbreakufboot" optional="True" type="float" min="0.01" max="0.99"/> 400 <param label="--p-stop-iter: INTEGER Number of unsuccessful iterations to stop. If not Range(1, None) set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pstopiter" optional="False" type="text" />
409 <param label="--p-allnni: --p-no-allnni Perform more thorough NNI search. [default: False]" name="pallnni" selected="False" type="boolean"/> 401 <param label="--p-perturb-nni-strength: NUMBER Range(0.01, 1.0) Perturbation strength for randomized NNI. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pperturbnnistrength" optional="False" type="text" />
410 <param label="--p-alrt: INTEGER Single branch test method. Number of bootstrap Range(1000, None) replicates to perform an SH-like approximate likelihood ratio test (SH-aLRT). Minimum of 1000 replicates is recomended. Set to '0' for parametric aLRT test. Can be used with other 'single branch test methods'. Values reported in the order of: alrt, lbp, abayes, ufboot. [optional]" name="palrt" optional="True" type="integer" min="1000"/> 402 <param label="--p-spr-radius: INTEGER Radius for parsimony SPR search. If not set, Range(1, None) program defaults will be used. See IQ-TREE manual for details. [optional]" name="psprradius" optional="False" type="text" />
411 <param label="--p-abayes: --p-no-abayes Single branch test method. Performs an approximate Bayes test. Can be used with other 'single branch test methods' and ultrafast bootstrap. Values reported in the order of: alrt, lbp, abayes, ufboot. [default: False]" name="pabayes" selected="False" type="boolean"/> 403 <param label="--p-n-max-ufboot-iter: INTEGER Range(1, None) Maximum number of iterations. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pnmaxufbootiter" optional="False" type="text" />
412 <param label="--p-lbp: INTEGER Single branch test method. Number of bootstrap Range(1000, None) replicates to perform a fast local bootstrap probability method. Minimum of 1000 replicates is recomended. Can be used with other 'single branch test methods'. Values reported in the order of: alrt, lbp, abayes, ufboot. [optional]" name="plbp" optional="True" type="integer" min="1000"/> 404 <param label="--p-n-ufboot-steps: INTEGER Range(1, None) Number of iterations for UFBoot stopping rule. If not set, program defaults will be used.See IQ-TREE manual for details. [optional]" name="pnufbootsteps" optional="False" type="text" />
413 <param label="--p-bnni: --p-no-bnni Optimize UFBoot trees by NNI on bootstrap alignment. This option reduces the risk of overestimating branch supports with UFBoot due to severe model violations. [default: False]" name="pbnni" selected="False" type="boolean"/> 405 <param label="--p-min-cor-ufboot: NUMBER Range(0.51, 0.99) Minimum correlation coefficient. If not set, program defaults will be used.See IQ-TREE manual for details. [optional]" name="pmincorufboot" optional="False" type="text" />
414 <param label="--p-safe: --p-no-safe Safe likelihood kernel to avoid numerical underflow. [default: False]" name="psafe" selected="False" type="boolean"/> 406 <param label="--p-ep-break-ufboot: NUMBER Range(0.01, 0.99) Epsilon value to break tie. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pepbreakufboot" optional="False" type="text" />
415 </inputs> 407 <param label="--p-allnni: --p-allnni: / --p-no-allnni Perform more thorough NNI search. [default: False]" name="pallnni" selected="False" type="boolean" />
416 <outputs> 408 <param label="--p-alrt: INTEGER Single branch test method. Number of bootstrap Range(1000, None) replicates to perform an SH-like approximate likelihood ratio test (SH-aLRT). Minimum of 1000 replicates is recomended. Can be used with other \'single branch test methods\'. Values reported in the order of: alrt, lbp, abayes. [optional]" name="palrt" optional="False" type="text" />
417 <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree"/> 409 <param label="--p-abayes: --p-abayes: / --p-no-abayes Single branch test method. Performs an approximate Bayes test. Can be used with other \'single branch test methods\' and ultrafast bootstrap. Values reported in the order of: alrt, lbp, abayes, ufboot. [default: False]" name="pabayes" selected="False" type="boolean" />
418 </outputs> 410 <param label="--p-lbp: INTEGER Single branch test method. Number of bootstrap Range(1000, None) replicates to perform a fast local bootstrap probability method. Minimum of 1000 replicates is recomended. Can be used with other \'single branch test methods\'. Values reported in the order of: alrt, lbp, abayes, ufboot. [optional]" name="plbp" optional="False" type="text" />
419 <help><![CDATA[ 411 <param label="--p-bnni: --p-bnni: / --p-no-bnni Optimize UFBoot trees by NNI on bootstrap alignment. This option reduces the risk of overestimating branch supports with UFBoot due to severe model violations. [default: False]" name="pbnni" selected="False" type="boolean" />
412 <param label="--p-safe: --p-safe: / --p-no-safe Safe likelihood kernel to avoid numerical underflow. [default: False]" name="psafe" selected="False" type="boolean" />
413 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
414
415 </inputs>
416
417 <outputs>
418 <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree" />
419
420 </outputs>
421
422 <help><![CDATA[
420 Construct a phylogenetic tree with IQ-TREE with bootstrap supports. 423 Construct a phylogenetic tree with IQ-TREE with bootstrap supports.
421 ################################################################### 424 ###############################################################
422 425
423 Construct a phylogenetic tree using IQ-TREE (http://www.iqtree.org/) with 426 Construct a phylogenetic tree using IQ-TREE (http://www.iqtree.org/) with
424 automatic model selection and bootstrap supports. 427 automatic model selection and bootstrap supports.
425 428
426 Parameters 429 Parameters
428 alignment : FeatureData[AlignedSequence] 431 alignment : FeatureData[AlignedSequence]
429 Aligned sequences to be used for phylogenetic reconstruction. 432 Aligned sequences to be used for phylogenetic reconstruction.
430 seed : Int, optional 433 seed : Int, optional
431 Random number seed. If not set, program defaults will be used. See IQ- 434 Random number seed. If not set, program defaults will be used. See IQ-
432 TREE manual for details. 435 TREE manual for details.
436 n_cores : Int % Range(1, None) | Str % Choices('auto'), optional
437 The number of cores to use for parallel processing. Use `auto` to let
438 IQ-TREE automatically determine the optimal number of cores to use.
439 n_cores_max : Int % Range(2, None), optional
440 Limits the maximum number of cores to be used when 'n_cores' is set to
441 'auto'.
433 n_runs : Int % Range(1, None), optional 442 n_runs : Int % Range(1, None), optional
434 Number of indepedent runs. Multiple independent runs (e.g. 10) can 443 Number of indepedent runs. Multiple independent runs (e.g. 10) can
435 outperform a single run in terms of likelihood maximisation. 444 outperform a single run in terms of likelihood maximisation.
436 substitution_model : Str % Choices('JC', 'JC+I', 'JC+G', 'JC+I+G', 'JC+R2', 'JC+R3', 'JC+R4', 'JC+R5', 'JC+R6', 'JC+R7', 'JC+R8', 'JC+R9', 'JC+R10', 'F81', 'F81+I', 'F81+G', 'F81+I+G', 'F81+R2', 'F81+R3', 'F81+R4', 'F81+R5', 'F81+R6', 'F81+R7', 'F81+R8', 'F81+R9', 'F81+R10', 'K80', 'K80+I', 'K80+G', 'K80+I+G', 'K80+R2', 'K80+R3', 'K80+R4', 'K80+R5', 'K80+R6', 'K80+R7', 'K80+R8', 'K80+R9', 'K80+R10', 'HKY', 'HKY+I', 'HKY+G', 'HKY+I+G', 'HKY+R2', 'HKY+R3', 'HKY+R4', 'HKY+R5', 'HKY+R6', 'HKY+R7', 'HKY+R8', 'HKY+R9', 'HKY+R10', 'TNe', 'TNe+I', 'TNe+G', 'TNe+I+G', 'TNe+R2', 'TNe+R3', 'TNe+R4', 'TNe+R5', 'TNe+R6', 'TNe+R7', 'TNe+R8', 'TNe+R9', 'TNe+R10', 'TN', 'TN+I', 'TN+G', 'TN+I+G', 'TN+R2', 'TN+R3', 'TN+R4', 'TN+R5', 'TN+R6', 'TN+R7', 'TN+R8', 'TN+R9', 'TN+R10', 'K81', 'K81+I', 'K81+G', 'K81+I+G', 'K81+R2', 'K81+R3', 'K81+R4', 'K81+R5', 'K81+R6', 'K81+R7', 'K81+R8', 'K81+R9', 'K81+R10', 'K81u', 'K81u+I', 'K81u+G', 'K81u+I+G', 'K81u+R2', 'K81u+R3', 'K81u+R4', 'K81u+R5', 'K81u+R6', 'K81u+R7', 'K81u+R8', 'K81u+R9', 'K81u+R10', 'TPM2', 'TPM2+I', 'TPM2+G', 'TPM2+I+G', 'TPM2+R2', 'TPM2+R3', 'TPM2+R4', 'TPM2+R5', 'TPM2+R6', 'TPM2+R7', 'TPM2+R8', 'TPM2+R9', 'TPM2+R10', 'TPM2u', 'TPM2u+I', 'TPM2u+G', 'TPM2u+I+G', 'TPM2u+R2', 'TPM2u+R3', 'TPM2u+R4', 'TPM2u+R5', 'TPM2u+R6', 'TPM2u+R7', 'TPM2u+R8', 'TPM2u+R9', 'TPM2u+R10', 'TPM3', 'TPM3+I', 'TPM3+G', 'TPM3+I+G', 'TPM3+R2', 'TPM3+R3', 'TPM3+R4', 'TPM3+R5', 'TPM3+R6', 'TPM3+R7', 'TPM3+R8', 'TPM3+R9', 'TPM3+R10', 'TPM3u', 'TPM3u+I', 'TPM3u+G', 'TPM3u+I+G', 'TPM3u+R2', 'TPM3u+R3', 'TPM3u+R4', 'TPM3u+R5', 'TPM3u+R6', 'TPM3u+R7', 'TPM3u+R8', 'TPM3u+R9', 'TPM3u+R10', 'TIMe', 'TIMe+I', 'TIMe+G', 'TIMe+I+G', 'TIMe+R2', 'TIMe+R3', 'TIMe+R4', 'TIMe+R5', 'TIMe+R6', 'TIMe+R7', 'TIMe+R8', 'TIMe+R9', 'TIMe+R10', 'TIM', 'TIM+I', 'TIM+G', 'TIM+I+G', 'TIM+R2', 'TIM+R3', 'TIM+R4', 'TIM+R5', 'TIM+R6', 'TIM+R7', 'TIM+R8', 'TIM+R9', 'TIM+R10', 'TIM2e', 'TIM2e+I', 'TIM2e+G', 'TIM2e+I+G', 'TIM2e+R2', 'TIM2e+R3', 'TIM2e+R4', 'TIM2e+R5', 'TIM2e+R6', 'TIM2e+R7', 'TIM2e+R8', 'TIM2e+R9', 'TIM2e+R10', 'TIM2', 'TIM2+I', 'TIM2+G', 'TIM2+I+G', 'TIM2+R2', 'TIM2+R3', 'TIM2+R4', 'TIM2+R5', 'TIM2+R6', 'TIM2+R7', 'TIM2+R8', 'TIM2+R9', 'TIM2+R10', 'TIM3e', 'TIM3e+I', 'TIM3e+G', 'TIM3e+I+G', 'TIM3e+R2', 'TIM3e+R3', 'TIM3e+R4', 'TIM3e+R5', 'TIM3e+R6', 'TIM3e+R7', 'TIM3e+R8', 'TIM3e+R9', 'TIM3e+R10', 'TIM3', 'TIM3+I', 'TIM3+G', 'TIM3+I+G', 'TIM3+R2', 'TIM3+R3', 'TIM3+R4', 'TIM3+R5', 'TIM3+R6', 'TIM3+R7', 'TIM3+R8', 'TIM3+R9', 'TIM3+R10', 'TVMe', 'TVMe+I', 'TVMe+G', 'TVMe+I+G', 'TVMe+R2', 'TVMe+R3', 'TVMe+R4', 'TVMe+R5', 'TVMe+R6', 'TVMe+R7', 'TVMe+R8', 'TVMe+R9', 'TVMe+R10', 'TVM', 'TVM+I', 'TVM+G', 'TVM+I+G', 'TVM+R2', 'TVM+R3', 'TVM+R4', 'TVM+R5', 'TVM+R6', 'TVM+R7', 'TVM+R8', 'TVM+R9', 'TVM+R10', 'SYM', 'SYM+I', 'SYM+G', 'SYM+I+G', 'SYM+R2', 'SYM+R3', 'SYM+R4', 'SYM+R5', 'SYM+R6', 'SYM+R7', 'SYM+R8', 'SYM+R9', 'SYM+R10', 'GTR', 'GTR+I', 'GTR+G', 'GTR+I+G', 'GTR+R2', 'GTR+R3', 'GTR+R4', 'GTR+R5', 'GTR+R6', 'GTR+R7', 'GTR+R8', 'GTR+R9', 'GTR+R10', 'MFP', 'TEST'), optional 445 substitution_model : Str % Choices('JC', 'JC+I', 'JC+G', 'JC+I+G', 'JC+R2', 'JC+R3', 'JC+R4', 'JC+R5', 'JC+R6', 'JC+R7', 'JC+R8', 'JC+R9', 'JC+R10', 'F81', 'F81+I', 'F81+G', 'F81+I+G', 'F81+R2', 'F81+R3', 'F81+R4', 'F81+R5', 'F81+R6', 'F81+R7', 'F81+R8', 'F81+R9', 'F81+R10', 'K80', 'K80+I', 'K80+G', 'K80+I+G', 'K80+R2', 'K80+R3', 'K80+R4', 'K80+R5', 'K80+R6', 'K80+R7', 'K80+R8', 'K80+R9', 'K80+R10', 'HKY', 'HKY+I', 'HKY+G', 'HKY+I+G', 'HKY+R2', 'HKY+R3', 'HKY+R4', 'HKY+R5', 'HKY+R6', 'HKY+R7', 'HKY+R8', 'HKY+R9', 'HKY+R10', 'TNe', 'TNe+I', 'TNe+G', 'TNe+I+G', 'TNe+R2', 'TNe+R3', 'TNe+R4', 'TNe+R5', 'TNe+R6', 'TNe+R7', 'TNe+R8', 'TNe+R9', 'TNe+R10', 'TN', 'TN+I', 'TN+G', 'TN+I+G', 'TN+R2', 'TN+R3', 'TN+R4', 'TN+R5', 'TN+R6', 'TN+R7', 'TN+R8', 'TN+R9', 'TN+R10', 'K81', 'K81+I', 'K81+G', 'K81+I+G', 'K81+R2', 'K81+R3', 'K81+R4', 'K81+R5', 'K81+R6', 'K81+R7', 'K81+R8', 'K81+R9', 'K81+R10', 'K81u', 'K81u+I', 'K81u+G', 'K81u+I+G', 'K81u+R2', 'K81u+R3', 'K81u+R4', 'K81u+R5', 'K81u+R6', 'K81u+R7', 'K81u+R8', 'K81u+R9', 'K81u+R10', 'TPM2', 'TPM2+I', 'TPM2+G', 'TPM2+I+G', 'TPM2+R2', 'TPM2+R3', 'TPM2+R4', 'TPM2+R5', 'TPM2+R6', 'TPM2+R7', 'TPM2+R8', 'TPM2+R9', 'TPM2+R10', 'TPM2u', 'TPM2u+I', 'TPM2u+G', 'TPM2u+I+G', 'TPM2u+R2', 'TPM2u+R3', 'TPM2u+R4', 'TPM2u+R5', 'TPM2u+R6', 'TPM2u+R7', 'TPM2u+R8', 'TPM2u+R9', 'TPM2u+R10', 'TPM3', 'TPM3+I', 'TPM3+G', 'TPM3+I+G', 'TPM3+R2', 'TPM3+R3', 'TPM3+R4', 'TPM3+R5', 'TPM3+R6', 'TPM3+R7', 'TPM3+R8', 'TPM3+R9', 'TPM3+R10', 'TPM3u', 'TPM3u+I', 'TPM3u+G', 'TPM3u+I+G', 'TPM3u+R2', 'TPM3u+R3', 'TPM3u+R4', 'TPM3u+R5', 'TPM3u+R6', 'TPM3u+R7', 'TPM3u+R8', 'TPM3u+R9', 'TPM3u+R10', 'TIMe', 'TIMe+I', 'TIMe+G', 'TIMe+I+G', 'TIMe+R2', 'TIMe+R3', 'TIMe+R4', 'TIMe+R5', 'TIMe+R6', 'TIMe+R7', 'TIMe+R8', 'TIMe+R9', 'TIMe+R10', 'TIM', 'TIM+I', 'TIM+G', 'TIM+I+G', 'TIM+R2', 'TIM+R3', 'TIM+R4', 'TIM+R5', 'TIM+R6', 'TIM+R7', 'TIM+R8', 'TIM+R9', 'TIM+R10', 'TIM2e', 'TIM2e+I', 'TIM2e+G', 'TIM2e+I+G', 'TIM2e+R2', 'TIM2e+R3', 'TIM2e+R4', 'TIM2e+R5', 'TIM2e+R6', 'TIM2e+R7', 'TIM2e+R8', 'TIM2e+R9', 'TIM2e+R10', 'TIM2', 'TIM2+I', 'TIM2+G', 'TIM2+I+G', 'TIM2+R2', 'TIM2+R3', 'TIM2+R4', 'TIM2+R5', 'TIM2+R6', 'TIM2+R7', 'TIM2+R8', 'TIM2+R9', 'TIM2+R10', 'TIM3e', 'TIM3e+I', 'TIM3e+G', 'TIM3e+I+G', 'TIM3e+R2', 'TIM3e+R3', 'TIM3e+R4', 'TIM3e+R5', 'TIM3e+R6', 'TIM3e+R7', 'TIM3e+R8', 'TIM3e+R9', 'TIM3e+R10', 'TIM3', 'TIM3+I', 'TIM3+G', 'TIM3+I+G', 'TIM3+R2', 'TIM3+R3', 'TIM3+R4', 'TIM3+R5', 'TIM3+R6', 'TIM3+R7', 'TIM3+R8', 'TIM3+R9', 'TIM3+R10', 'TVMe', 'TVMe+I', 'TVMe+G', 'TVMe+I+G', 'TVMe+R2', 'TVMe+R3', 'TVMe+R4', 'TVMe+R5', 'TVMe+R6', 'TVMe+R7', 'TVMe+R8', 'TVMe+R9', 'TVMe+R10', 'TVM', 'TVM+I', 'TVM+G', 'TVM+I+G', 'TVM+R2', 'TVM+R3', 'TVM+R4', 'TVM+R5', 'TVM+R6', 'TVM+R7', 'TVM+R8', 'TVM+R9', 'TVM+R10', 'SYM', 'SYM+I', 'SYM+G', 'SYM+I+G', 'SYM+R2', 'SYM+R3', 'SYM+R4', 'SYM+R5', 'SYM+R6', 'SYM+R7', 'SYM+R8', 'SYM+R9', 'SYM+R10', 'GTR', 'GTR+I', 'GTR+G', 'GTR+I+G', 'GTR+R2', 'GTR+R3', 'GTR+R4', 'GTR+R5', 'GTR+R6', 'GTR+R7', 'GTR+R8', 'GTR+R9', 'GTR+R10', 'MFP', 'TEST'), optional
437 Model of Nucleotide Substitution.If not provided, IQ-TREE will 446 Model of Nucleotide Substitution.If not provided, IQ-TREE will
449 Number of best trees retained during search. If not set, program 458 Number of best trees retained during search. If not set, program
450 defaults will be used. See IQ-TREE manual for details. 459 defaults will be used. See IQ-TREE manual for details.
451 stop_iter : Int % Range(1, None), optional 460 stop_iter : Int % Range(1, None), optional
452 Number of unsuccessful iterations to stop. If not set, program defaults 461 Number of unsuccessful iterations to stop. If not set, program defaults
453 will be used. See IQ-TREE manual for details. 462 will be used. See IQ-TREE manual for details.
454 perturb_nni_strength : Float % Range(0.01, 99), optional 463 perturb_nni_strength : Float % Range(0.01, 1.0), optional
455 Perturbation strength for randomized NNI. If not set, program defaults 464 Perturbation strength for randomized NNI. If not set, program defaults
456 will be used. See IQ-TREE manual for details. 465 will be used. See IQ-TREE manual for details.
457 spr_radius : Int % Range(1, None), optional 466 spr_radius : Int % Range(1, None), optional
458 Radius for parsimony SPR search. If not set, program defaults will be 467 Radius for parsimony SPR search. If not set, program defaults will be
459 used. See IQ-TREE manual for details. 468 used. See IQ-TREE manual for details.
472 allnni : Bool, optional 481 allnni : Bool, optional
473 Perform more thorough NNI search. 482 Perform more thorough NNI search.
474 alrt : Int % Range(1000, None), optional 483 alrt : Int % Range(1000, None), optional
475 Single branch test method. Number of bootstrap replicates to perform an 484 Single branch test method. Number of bootstrap replicates to perform an
476 SH-like approximate likelihood ratio test (SH-aLRT). Minimum of 1000 485 SH-like approximate likelihood ratio test (SH-aLRT). Minimum of 1000
477 replicates is recomended. Set to '0' for parametric aLRT test. Can be 486 replicates is recomended. Can be used with other 'single branch test
478 used with other 'single branch test methods'. Values reported in the 487 methods'. Values reported in the order of: alrt, lbp, abayes.
479 order of: alrt, lbp, abayes, ufboot.
480 abayes : Bool, optional 488 abayes : Bool, optional
481 Single branch test method. Performs an approximate Bayes test. Can be 489 Single branch test method. Performs an approximate Bayes test. Can be
482 used with other 'single branch test methods' and ultrafast bootstrap. 490 used with other 'single branch test methods' and ultrafast bootstrap.
483 Values reported in the order of: alrt, lbp, abayes, ufboot. 491 Values reported in the order of: alrt, lbp, abayes, ufboot.
484 lbp : Int % Range(1000, None), optional 492 lbp : Int % Range(1000, None), optional
495 503
496 Returns 504 Returns
497 ------- 505 -------
498 tree : Phylogeny[Unrooted] 506 tree : Phylogeny[Unrooted]
499 The resulting phylogenetic tree. 507 The resulting phylogenetic tree.
500 ]]></help> 508 ]]></help>
501 <macros> 509 <macros>
502 <import>qiime_citation.xml</import> 510 <import>qiime_citation.xml</import>
503 </macros> 511 </macros>
504 <expand macro="qiime_citation"/> 512 <expand macro="qiime_citation"/>
505 </tool> 513 </tool>