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comparison qiime2/qiime_phylogeny_iqtree.xml @ 14:a0a8d77a991c draft

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author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
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13:887cd4ad8e16 14:a0a8d77a991c
1 <?xml version="1.0" ?> 1 <?xml version="1.0" ?>
2 <tool id="qiime_phylogeny_iqtree" name="qiime phylogeny iqtree" version="2019.7"> 2 <tool id="qiime_phylogeny_iqtree" name="qiime phylogeny iqtree"
3 <description> - Construct a phylogenetic tree with IQ-TREE.</description> 3 version="2020.8">
4 <requirements> 4 <description>Construct a phylogenetic tree with IQ-TREE.</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 9 qiime phylogeny iqtree
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 #set $pncores = '${GALAXY_SLOTS:-4}' 17 --p-n-cores=$pncores
17 18 #end if
18 #if str($pncores): 19
19 --p-n-cores="$pncores" 20 #set $pncoresmax = '${GALAXY_SLOTS:-4}'
20 #end if 21
21 22 #if str($pncoresmax):
22 #if str($pnruns): 23 --p-n-cores-max=$pncoresmax
23 --p-n-runs=$pnruns 24 #end if
24 #end if 25
26 --p-n-runs=$pnruns
25 27
26 #if str($psubstitutionmodel) != 'None': 28 #if str($psubstitutionmodel) != 'None':
27 --p-substitution-model=$psubstitutionmodel 29 --p-substitution-model=$psubstitutionmodel
28 #end if 30 #end if
29 31
30 #if str($pninitparstrees): 32 #if str($pninitparstrees):
31 --p-n-init-pars-trees="$pninitparstrees" 33 --p-n-init-pars-trees=$pninitparstrees
32 #end if 34 #end if
33
34 #if str($pntopinittrees): 35 #if str($pntopinittrees):
35 --p-n-top-init-trees="$pntopinittrees" 36 --p-n-top-init-trees=$pntopinittrees
36 #end if 37 #end if
37
38 #if str($pnbestretaintrees): 38 #if str($pnbestretaintrees):
39 --p-n-best-retain-trees="$pnbestretaintrees" 39 --p-n-best-retain-trees=$pnbestretaintrees
40 #end if 40 #end if
41
42 #if str($pniter): 41 #if str($pniter):
43 --p-n-iter="$pniter" 42 --p-n-iter=$pniter
44 #end if 43 #end if
45
46 #if str($pstopiter): 44 #if str($pstopiter):
47 --p-stop-iter="$pstopiter" 45 --p-stop-iter=$pstopiter
48 #end if 46 #end if
49
50 #if str($pperturbnnistrength): 47 #if str($pperturbnnistrength):
51 --p-perturb-nni-strength="$pperturbnnistrength" 48 --p-perturb-nni-strength=$pperturbnnistrength
52 #end if 49 #end if
53
54 #if str($psprradius): 50 #if str($psprradius):
55 --p-spr-radius="$psprradius" 51 --p-spr-radius=$psprradius
56 #end if 52 #end if
57
58 #if $pallnni: 53 #if $pallnni:
59 --p-allnni 54 --p-allnni
60 #end if 55 #end if
61 56
62 #if $pfast: 57 #if $pfast:
63 --p-fast 58 --p-fast
64 #end if 59 #end if
65 60
66 #if str($palrt): 61 #if str($palrt):
67 --p-alrt="$palrt" 62 --p-alrt=$palrt
68 #end if 63 #end if
69
70 #if $pabayes: 64 #if $pabayes:
71 --p-abayes 65 --p-abayes
72 #end if 66 #end if
73 67
74 #if str($plbp): 68 #if str($plbp):
75 --p-lbp="$plbp" 69 --p-lbp=$plbp
76 #end if 70 #end if
77
78 #if $psafe: 71 #if $psafe:
79 --p-safe 72 --p-safe
80 #end if 73 #end if
81 74
82 --o-tree=otree 75 --o-tree=otree
76
77 #if str($examples) != 'None':
78 --examples=$examples
79 #end if
80
83 ; 81 ;
84 cp otree.qza $otree 82 cp otree.qza $otree
85 ]]></command> 83
86 <inputs> 84 ]]></command>
87 <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"/> 85 <inputs>
88 <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"/> 86 <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" />
89 <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" value="1" min="1"/> 87 <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" />
90 <param label="--p-substitution-model: " name="psubstitutionmodel" optional="True" type="select"> 88 <param label="--p-n-cores: " name="pncores" optional="True" type="select">
91 <option selected="True" value="None">Selection is Optional</option> 89 <option selected="True" value="None">Selection is Optional</option>
92 <option value="JC">JC</option> 90 <option value="Int % Range(1">Int % Range(1</option>
93 <option value="JC+I">JC+I</option> 91 <option value="None">None</option>
94 <option value="JC+G">JC+G</option> 92 </param>
95 <option value="JC+I+G">JC+I+G</option> 93 <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" />
96 <option value="JC+R2">JC+R2</option> 94 <param label="--p-substitution-model: " name="psubstitutionmodel" optional="True" type="select">
97 <option value="JC+R3">JC+R3</option> 95 <option selected="True" value="None">Selection is Optional</option>
98 <option value="JC+R4">JC+R4</option> 96 <option value="JC">JC</option>
99 <option value="JC+R5">JC+R5</option> 97 <option value="JC+I">JC+I</option>
100 <option value="JC+R6">JC+R6</option> 98 <option value="JC+G">JC+G</option>
101 <option value="JC+R7">JC+R7</option> 99 <option value="JC+I+G">JC+I+G</option>
102 <option value="JC+R8">JC+R8</option> 100 <option value="JC+R2">JC+R2</option>
103 <option value="JC+R9">JC+R9</option> 101 <option value="JC+R3">JC+R3</option>
104 <option value="JC+R10">JC+R10</option> 102 <option value="JC+R4">JC+R4</option>
105 <option value="F81">F81</option> 103 <option value="JC+R5">JC+R5</option>
106 <option value="F81+I">F81+I</option> 104 <option value="JC+R6">JC+R6</option>
107 <option value="F81+G">F81+G</option> 105 <option value="JC+R7">JC+R7</option>
108 <option value="F81+I+G">F81+I+G</option> 106 <option value="JC+R8">JC+R8</option>
109 <option value="F81+R2">F81+R2</option> 107 <option value="JC+R9">JC+R9</option>
110 <option value="F81+R3">F81+R3</option> 108 <option value="JC+R10">JC+R10</option>
111 <option value="F81+R4">F81+R4</option> 109 <option value="F81">F81</option>
112 <option value="F81+R5">F81+R5</option> 110 <option value="F81+I">F81+I</option>
113 <option value="F81+R6">F81+R6</option> 111 <option value="F81+G">F81+G</option>
114 <option value="F81+R7">F81+R7</option> 112 <option value="F81+I+G">F81+I+G</option>
115 <option value="F81+R8">F81+R8</option> 113 <option value="F81+R2">F81+R2</option>
116 <option value="F81+R9">F81+R9</option> 114 <option value="F81+R3">F81+R3</option>
117 <option value="F81+R10">F81+R10</option> 115 <option value="F81+R4">F81+R4</option>
118 <option value="K80">K80</option> 116 <option value="F81+R5">F81+R5</option>
119 <option value="K80+I">K80+I</option> 117 <option value="F81+R6">F81+R6</option>
120 <option value="K80+G">K80+G</option> 118 <option value="F81+R7">F81+R7</option>
121 <option value="K80+I+G">K80+I+G</option> 119 <option value="F81+R8">F81+R8</option>
122 <option value="K80+R2">K80+R2</option> 120 <option value="F81+R9">F81+R9</option>
123 <option value="K80+R3">K80+R3</option> 121 <option value="F81+R10">F81+R10</option>
124 <option value="K80+R4">K80+R4</option> 122 <option value="K80">K80</option>
125 <option value="K80+R5">K80+R5</option> 123 <option value="K80+I">K80+I</option>
126 <option value="K80+R6">K80+R6</option> 124 <option value="K80+G">K80+G</option>
127 <option value="K80+R7">K80+R7</option> 125 <option value="K80+I+G">K80+I+G</option>
128 <option value="K80+R8">K80+R8</option> 126 <option value="K80+R2">K80+R2</option>
129 <option value="K80+R9">K80+R9</option> 127 <option value="K80+R3">K80+R3</option>
130 <option value="K80+R10">K80+R10</option> 128 <option value="K80+R4">K80+R4</option>
131 <option value="HKY">HKY</option> 129 <option value="K80+R5">K80+R5</option>
132 <option value="HKY+I">HKY+I</option> 130 <option value="K80+R6">K80+R6</option>
133 <option value="HKY+G">HKY+G</option> 131 <option value="K80+R7">K80+R7</option>
134 <option value="HKY+I+G">HKY+I+G</option> 132 <option value="K80+R8">K80+R8</option>
135 <option value="HKY+R2">HKY+R2</option> 133 <option value="K80+R9">K80+R9</option>
136 <option value="HKY+R3">HKY+R3</option> 134 <option value="K80+R10">K80+R10</option>
137 <option value="HKY+R4">HKY+R4</option> 135 <option value="HKY">HKY</option>
138 <option value="HKY+R5">HKY+R5</option> 136 <option value="HKY+I">HKY+I</option>
139 <option value="HKY+R6">HKY+R6</option> 137 <option value="HKY+G">HKY+G</option>
140 <option value="HKY+R7">HKY+R7</option> 138 <option value="HKY+I+G">HKY+I+G</option>
141 <option value="HKY+R8">HKY+R8</option> 139 <option value="HKY+R2">HKY+R2</option>
142 <option value="HKY+R9">HKY+R9</option> 140 <option value="HKY+R3">HKY+R3</option>
143 <option value="HKY+R10">HKY+R10</option> 141 <option value="HKY+R4">HKY+R4</option>
144 <option value="TNe">TNe</option> 142 <option value="HKY+R5">HKY+R5</option>
145 <option value="TNe+I">TNe+I</option> 143 <option value="HKY+R6">HKY+R6</option>
146 <option value="TNe+G">TNe+G</option> 144 <option value="HKY+R7">HKY+R7</option>
147 <option value="TNe+I+G">TNe+I+G</option> 145 <option value="HKY+R8">HKY+R8</option>
148 <option value="TNe+R2">TNe+R2</option> 146 <option value="HKY+R9">HKY+R9</option>
149 <option value="TNe+R3">TNe+R3</option> 147 <option value="HKY+R10">HKY+R10</option>
150 <option value="TNe+R4">TNe+R4</option> 148 <option value="TNe">TNe</option>
151 <option value="TNe+R5">TNe+R5</option> 149 <option value="TNe+I">TNe+I</option>
152 <option value="TNe+R6">TNe+R6</option> 150 <option value="TNe+G">TNe+G</option>
153 <option value="TNe+R7">TNe+R7</option> 151 <option value="TNe+I+G">TNe+I+G</option>
154 <option value="TNe+R8">TNe+R8</option> 152 <option value="TNe+R2">TNe+R2</option>
155 <option value="TNe+R9">TNe+R9</option> 153 <option value="TNe+R3">TNe+R3</option>
156 <option value="TNe+R10">TNe+R10</option> 154 <option value="TNe+R4">TNe+R4</option>
157 <option value="TN">TN</option> 155 <option value="TNe+R5">TNe+R5</option>
158 <option value="TN+I">TN+I</option> 156 <option value="TNe+R6">TNe+R6</option>
159 <option value="TN+G">TN+G</option> 157 <option value="TNe+R7">TNe+R7</option>
160 <option value="TN+I+G">TN+I+G</option> 158 <option value="TNe+R8">TNe+R8</option>
161 <option value="TN+R2">TN+R2</option> 159 <option value="TNe+R9">TNe+R9</option>
162 <option value="TN+R3">TN+R3</option> 160 <option value="TNe+R10">TNe+R10</option>
163 <option value="TN+R4">TN+R4</option> 161 <option value="TN">TN</option>
164 <option value="TN+R5">TN+R5</option> 162 <option value="TN+I">TN+I</option>
165 <option value="TN+R6">TN+R6</option> 163 <option value="TN+G">TN+G</option>
166 <option value="TN+R7">TN+R7</option> 164 <option value="TN+I+G">TN+I+G</option>
167 <option value="TN+R8">TN+R8</option> 165 <option value="TN+R2">TN+R2</option>
168 <option value="TN+R9">TN+R9</option> 166 <option value="TN+R3">TN+R3</option>
169 <option value="TN+R10">TN+R10</option> 167 <option value="TN+R4">TN+R4</option>
170 <option value="K81">K81</option> 168 <option value="TN+R5">TN+R5</option>
171 <option value="K81+I">K81+I</option> 169 <option value="TN+R6">TN+R6</option>
172 <option value="K81+G">K81+G</option> 170 <option value="TN+R7">TN+R7</option>
173 <option value="K81+I+G">K81+I+G</option> 171 <option value="TN+R8">TN+R8</option>
174 <option value="K81+R2">K81+R2</option> 172 <option value="TN+R9">TN+R9</option>
175 <option value="K81+R3">K81+R3</option> 173 <option value="TN+R10">TN+R10</option>
176 <option value="K81+R4">K81+R4</option> 174 <option value="K81">K81</option>
177 <option value="K81+R5">K81+R5</option> 175 <option value="K81+I">K81+I</option>
178 <option value="K81+R6">K81+R6</option> 176 <option value="K81+G">K81+G</option>
179 <option value="K81+R7">K81+R7</option> 177 <option value="K81+I+G">K81+I+G</option>
180 <option value="K81+R8">K81+R8</option> 178 <option value="K81+R2">K81+R2</option>
181 <option value="K81+R9">K81+R9</option> 179 <option value="K81+R3">K81+R3</option>
182 <option value="K81+R10">K81+R10</option> 180 <option value="K81+R4">K81+R4</option>
183 <option value="K81u">K81u</option> 181 <option value="K81+R5">K81+R5</option>
184 <option value="K81u+I">K81u+I</option> 182 <option value="K81+R6">K81+R6</option>
185 <option value="K81u+G">K81u+G</option> 183 <option value="K81+R7">K81+R7</option>
186 <option value="K81u+I+G">K81u+I+G</option> 184 <option value="K81+R8">K81+R8</option>
187 <option value="K81u+R2">K81u+R2</option> 185 <option value="K81+R9">K81+R9</option>
188 <option value="K81u+R3">K81u+R3</option> 186 <option value="K81+R10">K81+R10</option>
189 <option value="K81u+R4">K81u+R4</option> 187 <option value="K81u">K81u</option>
190 <option value="K81u+R5">K81u+R5</option> 188 <option value="K81u+I">K81u+I</option>
191 <option value="K81u+R6">K81u+R6</option> 189 <option value="K81u+G">K81u+G</option>
192 <option value="K81u+R7">K81u+R7</option> 190 <option value="K81u+I+G">K81u+I+G</option>
193 <option value="K81u+R8">K81u+R8</option> 191 <option value="K81u+R2">K81u+R2</option>
194 <option value="K81u+R9">K81u+R9</option> 192 <option value="K81u+R3">K81u+R3</option>
195 <option value="K81u+R10">K81u+R10</option> 193 <option value="K81u+R4">K81u+R4</option>
196 <option value="TPM2">TPM2</option> 194 <option value="K81u+R5">K81u+R5</option>
197 <option value="TPM2+I">TPM2+I</option> 195 <option value="K81u+R6">K81u+R6</option>
198 <option value="TPM2+G">TPM2+G</option> 196 <option value="K81u+R7">K81u+R7</option>
199 <option value="TPM2+I+G">TPM2+I+G</option> 197 <option value="K81u+R8">K81u+R8</option>
200 <option value="TPM2+R2">TPM2+R2</option> 198 <option value="K81u+R9">K81u+R9</option>
201 <option value="TPM2+R3">TPM2+R3</option> 199 <option value="K81u+R10">K81u+R10</option>
202 <option value="TPM2+R4">TPM2+R4</option> 200 <option value="TPM2">TPM2</option>
203 <option value="TPM2+R5">TPM2+R5</option> 201 <option value="TPM2+I">TPM2+I</option>
204 <option value="TPM2+R6">TPM2+R6</option> 202 <option value="TPM2+G">TPM2+G</option>
205 <option value="TPM2+R7">TPM2+R7</option> 203 <option value="TPM2+I+G">TPM2+I+G</option>
206 <option value="TPM2+R8">TPM2+R8</option> 204 <option value="TPM2+R2">TPM2+R2</option>
207 <option value="TPM2+R9">TPM2+R9</option> 205 <option value="TPM2+R3">TPM2+R3</option>
208 <option value="TPM2+R10">TPM2+R10</option> 206 <option value="TPM2+R4">TPM2+R4</option>
209 <option value="TPM2u">TPM2u</option> 207 <option value="TPM2+R5">TPM2+R5</option>
210 <option value="TPM2u+I">TPM2u+I</option> 208 <option value="TPM2+R6">TPM2+R6</option>
211 <option value="TPM2u+G">TPM2u+G</option> 209 <option value="TPM2+R7">TPM2+R7</option>
212 <option value="TPM2u+I+G">TPM2u+I+G</option> 210 <option value="TPM2+R8">TPM2+R8</option>
213 <option value="TPM2u+R2">TPM2u+R2</option> 211 <option value="TPM2+R9">TPM2+R9</option>
214 <option value="TPM2u+R3">TPM2u+R3</option> 212 <option value="TPM2+R10">TPM2+R10</option>
215 <option value="TPM2u+R4">TPM2u+R4</option> 213 <option value="TPM2u">TPM2u</option>
216 <option value="TPM2u+R5">TPM2u+R5</option> 214 <option value="TPM2u+I">TPM2u+I</option>
217 <option value="TPM2u+R6">TPM2u+R6</option> 215 <option value="TPM2u+G">TPM2u+G</option>
218 <option value="TPM2u+R7">TPM2u+R7</option> 216 <option value="TPM2u+I+G">TPM2u+I+G</option>
219 <option value="TPM2u+R8">TPM2u+R8</option> 217 <option value="TPM2u+R2">TPM2u+R2</option>
220 <option value="TPM2u+R9">TPM2u+R9</option> 218 <option value="TPM2u+R3">TPM2u+R3</option>
221 <option value="TPM2u+R10">TPM2u+R10</option> 219 <option value="TPM2u+R4">TPM2u+R4</option>
222 <option value="TPM3">TPM3</option> 220 <option value="TPM2u+R5">TPM2u+R5</option>
223 <option value="TPM3+I">TPM3+I</option> 221 <option value="TPM2u+R6">TPM2u+R6</option>
224 <option value="TPM3+G">TPM3+G</option> 222 <option value="TPM2u+R7">TPM2u+R7</option>
225 <option value="TPM3+I+G">TPM3+I+G</option> 223 <option value="TPM2u+R8">TPM2u+R8</option>
226 <option value="TPM3+R2">TPM3+R2</option> 224 <option value="TPM2u+R9">TPM2u+R9</option>
227 <option value="TPM3+R3">TPM3+R3</option> 225 <option value="TPM2u+R10">TPM2u+R10</option>
228 <option value="TPM3+R4">TPM3+R4</option> 226 <option value="TPM3">TPM3</option>
229 <option value="TPM3+R5">TPM3+R5</option> 227 <option value="TPM3+I">TPM3+I</option>
230 <option value="TPM3+R6">TPM3+R6</option> 228 <option value="TPM3+G">TPM3+G</option>
231 <option value="TPM3+R7">TPM3+R7</option> 229 <option value="TPM3+I+G">TPM3+I+G</option>
232 <option value="TPM3+R8">TPM3+R8</option> 230 <option value="TPM3+R2">TPM3+R2</option>
233 <option value="TPM3+R9">TPM3+R9</option> 231 <option value="TPM3+R3">TPM3+R3</option>
234 <option value="TPM3+R10">TPM3+R10</option> 232 <option value="TPM3+R4">TPM3+R4</option>
235 <option value="TPM3u">TPM3u</option> 233 <option value="TPM3+R5">TPM3+R5</option>
236 <option value="TPM3u+I">TPM3u+I</option> 234 <option value="TPM3+R6">TPM3+R6</option>
237 <option value="TPM3u+G">TPM3u+G</option> 235 <option value="TPM3+R7">TPM3+R7</option>
238 <option value="TPM3u+I+G">TPM3u+I+G</option> 236 <option value="TPM3+R8">TPM3+R8</option>
239 <option value="TPM3u+R2">TPM3u+R2</option> 237 <option value="TPM3+R9">TPM3+R9</option>
240 <option value="TPM3u+R3">TPM3u+R3</option> 238 <option value="TPM3+R10">TPM3+R10</option>
241 <option value="TPM3u+R4">TPM3u+R4</option> 239 <option value="TPM3u">TPM3u</option>
242 <option value="TPM3u+R5">TPM3u+R5</option> 240 <option value="TPM3u+I">TPM3u+I</option>
243 <option value="TPM3u+R6">TPM3u+R6</option> 241 <option value="TPM3u+G">TPM3u+G</option>
244 <option value="TPM3u+R7">TPM3u+R7</option> 242 <option value="TPM3u+I+G">TPM3u+I+G</option>
245 <option value="TPM3u+R8">TPM3u+R8</option> 243 <option value="TPM3u+R2">TPM3u+R2</option>
246 <option value="TPM3u+R9">TPM3u+R9</option> 244 <option value="TPM3u+R3">TPM3u+R3</option>
247 <option value="TPM3u+R10">TPM3u+R10</option> 245 <option value="TPM3u+R4">TPM3u+R4</option>
248 <option value="TIMe">TIMe</option> 246 <option value="TPM3u+R5">TPM3u+R5</option>
249 <option value="TIMe+I">TIMe+I</option> 247 <option value="TPM3u+R6">TPM3u+R6</option>
250 <option value="TIMe+G">TIMe+G</option> 248 <option value="TPM3u+R7">TPM3u+R7</option>
251 <option value="TIMe+I+G">TIMe+I+G</option> 249 <option value="TPM3u+R8">TPM3u+R8</option>
252 <option value="TIMe+R2">TIMe+R2</option> 250 <option value="TPM3u+R9">TPM3u+R9</option>
253 <option value="TIMe+R3">TIMe+R3</option> 251 <option value="TPM3u+R10">TPM3u+R10</option>
254 <option value="TIMe+R4">TIMe+R4</option> 252 <option value="TIMe">TIMe</option>
255 <option value="TIMe+R5">TIMe+R5</option> 253 <option value="TIMe+I">TIMe+I</option>
256 <option value="TIMe+R6">TIMe+R6</option> 254 <option value="TIMe+G">TIMe+G</option>
257 <option value="TIMe+R7">TIMe+R7</option> 255 <option value="TIMe+I+G">TIMe+I+G</option>
258 <option value="TIMe+R8">TIMe+R8</option> 256 <option value="TIMe+R2">TIMe+R2</option>
259 <option value="TIMe+R9">TIMe+R9</option> 257 <option value="TIMe+R3">TIMe+R3</option>
260 <option value="TIMe+R10">TIMe+R10</option> 258 <option value="TIMe+R4">TIMe+R4</option>
261 <option value="TIM">TIM</option> 259 <option value="TIMe+R5">TIMe+R5</option>
262 <option value="TIM+I">TIM+I</option> 260 <option value="TIMe+R6">TIMe+R6</option>
263 <option value="TIM+G">TIM+G</option> 261 <option value="TIMe+R7">TIMe+R7</option>
264 <option value="TIM+I+G">TIM+I+G</option> 262 <option value="TIMe+R8">TIMe+R8</option>
265 <option value="TIM+R2">TIM+R2</option> 263 <option value="TIMe+R9">TIMe+R9</option>
266 <option value="TIM+R3">TIM+R3</option> 264 <option value="TIMe+R10">TIMe+R10</option>
267 <option value="TIM+R4">TIM+R4</option> 265 <option value="TIM">TIM</option>
268 <option value="TIM+R5">TIM+R5</option> 266 <option value="TIM+I">TIM+I</option>
269 <option value="TIM+R6">TIM+R6</option> 267 <option value="TIM+G">TIM+G</option>
270 <option value="TIM+R7">TIM+R7</option> 268 <option value="TIM+I+G">TIM+I+G</option>
271 <option value="TIM+R8">TIM+R8</option> 269 <option value="TIM+R2">TIM+R2</option>
272 <option value="TIM+R9">TIM+R9</option> 270 <option value="TIM+R3">TIM+R3</option>
273 <option value="TIM+R10">TIM+R10</option> 271 <option value="TIM+R4">TIM+R4</option>
274 <option value="TIM2e">TIM2e</option> 272 <option value="TIM+R5">TIM+R5</option>
275 <option value="TIM2e+I">TIM2e+I</option> 273 <option value="TIM+R6">TIM+R6</option>
276 <option value="TIM2e+G">TIM2e+G</option> 274 <option value="TIM+R7">TIM+R7</option>
277 <option value="TIM2e+I+G">TIM2e+I+G</option> 275 <option value="TIM+R8">TIM+R8</option>
278 <option value="TIM2e+R2">TIM2e+R2</option> 276 <option value="TIM+R9">TIM+R9</option>
279 <option value="TIM2e+R3">TIM2e+R3</option> 277 <option value="TIM+R10">TIM+R10</option>
280 <option value="TIM2e+R4">TIM2e+R4</option> 278 <option value="TIM2e">TIM2e</option>
281 <option value="TIM2e+R5">TIM2e+R5</option> 279 <option value="TIM2e+I">TIM2e+I</option>
282 <option value="TIM2e+R6">TIM2e+R6</option> 280 <option value="TIM2e+G">TIM2e+G</option>
283 <option value="TIM2e+R7">TIM2e+R7</option> 281 <option value="TIM2e+I+G">TIM2e+I+G</option>
284 <option value="TIM2e+R8">TIM2e+R8</option> 282 <option value="TIM2e+R2">TIM2e+R2</option>
285 <option value="TIM2e+R9">TIM2e+R9</option> 283 <option value="TIM2e+R3">TIM2e+R3</option>
286 <option value="TIM2e+R10">TIM2e+R10</option> 284 <option value="TIM2e+R4">TIM2e+R4</option>
287 <option value="TIM2">TIM2</option> 285 <option value="TIM2e+R5">TIM2e+R5</option>
288 <option value="TIM2+I">TIM2+I</option> 286 <option value="TIM2e+R6">TIM2e+R6</option>
289 <option value="TIM2+G">TIM2+G</option> 287 <option value="TIM2e+R7">TIM2e+R7</option>
290 <option value="TIM2+I+G">TIM2+I+G</option> 288 <option value="TIM2e+R8">TIM2e+R8</option>
291 <option value="TIM2+R2">TIM2+R2</option> 289 <option value="TIM2e+R9">TIM2e+R9</option>
292 <option value="TIM2+R3">TIM2+R3</option> 290 <option value="TIM2e+R10">TIM2e+R10</option>
293 <option value="TIM2+R4">TIM2+R4</option> 291 <option value="TIM2">TIM2</option>
294 <option value="TIM2+R5">TIM2+R5</option> 292 <option value="TIM2+I">TIM2+I</option>
295 <option value="TIM2+R6">TIM2+R6</option> 293 <option value="TIM2+G">TIM2+G</option>
296 <option value="TIM2+R7">TIM2+R7</option> 294 <option value="TIM2+I+G">TIM2+I+G</option>
297 <option value="TIM2+R8">TIM2+R8</option> 295 <option value="TIM2+R2">TIM2+R2</option>
298 <option value="TIM2+R9">TIM2+R9</option> 296 <option value="TIM2+R3">TIM2+R3</option>
299 <option value="TIM2+R10">TIM2+R10</option> 297 <option value="TIM2+R4">TIM2+R4</option>
300 <option value="TIM3e">TIM3e</option> 298 <option value="TIM2+R5">TIM2+R5</option>
301 <option value="TIM3e+I">TIM3e+I</option> 299 <option value="TIM2+R6">TIM2+R6</option>
302 <option value="TIM3e+G">TIM3e+G</option> 300 <option value="TIM2+R7">TIM2+R7</option>
303 <option value="TIM3e+I+G">TIM3e+I+G</option> 301 <option value="TIM2+R8">TIM2+R8</option>
304 <option value="TIM3e+R2">TIM3e+R2</option> 302 <option value="TIM2+R9">TIM2+R9</option>
305 <option value="TIM3e+R3">TIM3e+R3</option> 303 <option value="TIM2+R10">TIM2+R10</option>
306 <option value="TIM3e+R4">TIM3e+R4</option> 304 <option value="TIM3e">TIM3e</option>
307 <option value="TIM3e+R5">TIM3e+R5</option> 305 <option value="TIM3e+I">TIM3e+I</option>
308 <option value="TIM3e+R6">TIM3e+R6</option> 306 <option value="TIM3e+G">TIM3e+G</option>
309 <option value="TIM3e+R7">TIM3e+R7</option> 307 <option value="TIM3e+I+G">TIM3e+I+G</option>
310 <option value="TIM3e+R8">TIM3e+R8</option> 308 <option value="TIM3e+R2">TIM3e+R2</option>
311 <option value="TIM3e+R9">TIM3e+R9</option> 309 <option value="TIM3e+R3">TIM3e+R3</option>
312 <option value="TIM3e+R10">TIM3e+R10</option> 310 <option value="TIM3e+R4">TIM3e+R4</option>
313 <option value="TIM3">TIM3</option> 311 <option value="TIM3e+R5">TIM3e+R5</option>
314 <option value="TIM3+I">TIM3+I</option> 312 <option value="TIM3e+R6">TIM3e+R6</option>
315 <option value="TIM3+G">TIM3+G</option> 313 <option value="TIM3e+R7">TIM3e+R7</option>
316 <option value="TIM3+I+G">TIM3+I+G</option> 314 <option value="TIM3e+R8">TIM3e+R8</option>
317 <option value="TIM3+R2">TIM3+R2</option> 315 <option value="TIM3e+R9">TIM3e+R9</option>
318 <option value="TIM3+R3">TIM3+R3</option> 316 <option value="TIM3e+R10">TIM3e+R10</option>
319 <option value="TIM3+R4">TIM3+R4</option> 317 <option value="TIM3">TIM3</option>
320 <option value="TIM3+R5">TIM3+R5</option> 318 <option value="TIM3+I">TIM3+I</option>
321 <option value="TIM3+R6">TIM3+R6</option> 319 <option value="TIM3+G">TIM3+G</option>
322 <option value="TIM3+R7">TIM3+R7</option> 320 <option value="TIM3+I+G">TIM3+I+G</option>
323 <option value="TIM3+R8">TIM3+R8</option> 321 <option value="TIM3+R2">TIM3+R2</option>
324 <option value="TIM3+R9">TIM3+R9</option> 322 <option value="TIM3+R3">TIM3+R3</option>
325 <option value="TIM3+R10">TIM3+R10</option> 323 <option value="TIM3+R4">TIM3+R4</option>
326 <option value="TVMe">TVMe</option> 324 <option value="TIM3+R5">TIM3+R5</option>
327 <option value="TVMe+I">TVMe+I</option> 325 <option value="TIM3+R6">TIM3+R6</option>
328 <option value="TVMe+G">TVMe+G</option> 326 <option value="TIM3+R7">TIM3+R7</option>
329 <option value="TVMe+I+G">TVMe+I+G</option> 327 <option value="TIM3+R8">TIM3+R8</option>
330 <option value="TVMe+R2">TVMe+R2</option> 328 <option value="TIM3+R9">TIM3+R9</option>
331 <option value="TVMe+R3">TVMe+R3</option> 329 <option value="TIM3+R10">TIM3+R10</option>
332 <option value="TVMe+R4">TVMe+R4</option> 330 <option value="TVMe">TVMe</option>
333 <option value="TVMe+R5">TVMe+R5</option> 331 <option value="TVMe+I">TVMe+I</option>
334 <option value="TVMe+R6">TVMe+R6</option> 332 <option value="TVMe+G">TVMe+G</option>
335 <option value="TVMe+R7">TVMe+R7</option> 333 <option value="TVMe+I+G">TVMe+I+G</option>
336 <option value="TVMe+R8">TVMe+R8</option> 334 <option value="TVMe+R2">TVMe+R2</option>
337 <option value="TVMe+R9">TVMe+R9</option> 335 <option value="TVMe+R3">TVMe+R3</option>
338 <option value="TVMe+R10">TVMe+R10</option> 336 <option value="TVMe+R4">TVMe+R4</option>
339 <option value="TVM">TVM</option> 337 <option value="TVMe+R5">TVMe+R5</option>
340 <option value="TVM+I">TVM+I</option> 338 <option value="TVMe+R6">TVMe+R6</option>
341 <option value="TVM+G">TVM+G</option> 339 <option value="TVMe+R7">TVMe+R7</option>
342 <option value="TVM+I+G">TVM+I+G</option> 340 <option value="TVMe+R8">TVMe+R8</option>
343 <option value="TVM+R2">TVM+R2</option> 341 <option value="TVMe+R9">TVMe+R9</option>
344 <option value="TVM+R3">TVM+R3</option> 342 <option value="TVMe+R10">TVMe+R10</option>
345 <option value="TVM+R4">TVM+R4</option> 343 <option value="TVM">TVM</option>
346 <option value="TVM+R5">TVM+R5</option> 344 <option value="TVM+I">TVM+I</option>
347 <option value="TVM+R6">TVM+R6</option> 345 <option value="TVM+G">TVM+G</option>
348 <option value="TVM+R7">TVM+R7</option> 346 <option value="TVM+I+G">TVM+I+G</option>
349 <option value="TVM+R8">TVM+R8</option> 347 <option value="TVM+R2">TVM+R2</option>
350 <option value="TVM+R9">TVM+R9</option> 348 <option value="TVM+R3">TVM+R3</option>
351 <option value="TVM+R10">TVM+R10</option> 349 <option value="TVM+R4">TVM+R4</option>
352 <option value="SYM">SYM</option> 350 <option value="TVM+R5">TVM+R5</option>
353 <option value="SYM+I">SYM+I</option> 351 <option value="TVM+R6">TVM+R6</option>
354 <option value="SYM+G">SYM+G</option> 352 <option value="TVM+R7">TVM+R7</option>
355 <option value="SYM+I+G">SYM+I+G</option> 353 <option value="TVM+R8">TVM+R8</option>
356 <option value="SYM+R2">SYM+R2</option> 354 <option value="TVM+R9">TVM+R9</option>
357 <option value="SYM+R3">SYM+R3</option> 355 <option value="TVM+R10">TVM+R10</option>
358 <option value="SYM+R4">SYM+R4</option> 356 <option value="SYM">SYM</option>
359 <option value="SYM+R5">SYM+R5</option> 357 <option value="SYM+I">SYM+I</option>
360 <option value="SYM+R6">SYM+R6</option> 358 <option value="SYM+G">SYM+G</option>
361 <option value="SYM+R7">SYM+R7</option> 359 <option value="SYM+I+G">SYM+I+G</option>
362 <option value="SYM+R8">SYM+R8</option> 360 <option value="SYM+R2">SYM+R2</option>
363 <option value="SYM+R9">SYM+R9</option> 361 <option value="SYM+R3">SYM+R3</option>
364 <option value="SYM+R10">SYM+R10</option> 362 <option value="SYM+R4">SYM+R4</option>
365 <option value="GTR">GTR</option> 363 <option value="SYM+R5">SYM+R5</option>
366 <option value="GTR+I">GTR+I</option> 364 <option value="SYM+R6">SYM+R6</option>
367 <option value="GTR+G">GTR+G</option> 365 <option value="SYM+R7">SYM+R7</option>
368 <option value="GTR+I+G">GTR+I+G</option> 366 <option value="SYM+R8">SYM+R8</option>
369 <option value="GTR+R2">GTR+R2</option> 367 <option value="SYM+R9">SYM+R9</option>
370 <option value="GTR+R3">GTR+R3</option> 368 <option value="SYM+R10">SYM+R10</option>
371 <option value="GTR+R4">GTR+R4</option> 369 <option value="GTR">GTR</option>
372 <option value="GTR+R5">GTR+R5</option> 370 <option value="GTR+I">GTR+I</option>
373 <option value="GTR+R6">GTR+R6</option> 371 <option value="GTR+G">GTR+G</option>
374 <option value="GTR+R7">GTR+R7</option> 372 <option value="GTR+I+G">GTR+I+G</option>
375 <option value="GTR+R8">GTR+R8</option> 373 <option value="GTR+R2">GTR+R2</option>
376 <option value="GTR+R9">GTR+R9</option> 374 <option value="GTR+R3">GTR+R3</option>
377 <option value="GTR+R10">GTR+R10</option> 375 <option value="GTR+R4">GTR+R4</option>
378 <option value="MFP">MFP</option> 376 <option value="GTR+R5">GTR+R5</option>
379 <option value="TEST">TEST</option> 377 <option value="GTR+R6">GTR+R6</option>
380 </param> 378 <option value="GTR+R7">GTR+R7</option>
381 <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"/> 379 <option value="GTR+R8">GTR+R8</option>
382 <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"/> 380 <option value="GTR+R9">GTR+R9</option>
383 <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"/> 381 <option value="GTR+R10">GTR+R10</option>
384 <param label="--p-n-iter: INTEGER Fix number of iterations to stop. If not set, Range(1, None) program defaults will be used. See IQ-TREE manual for details. [optional]" name="pniter" optional="True" type="integer" min="1"/> 382 <option value="MFP">MFP</option>
385 <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"/> 383 <option value="TEST">TEST</option>
386 <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"/> 384 </param>
387 <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"/> 385 <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" />
388 <param label="--p-allnni: --p-no-allnni Perform more thorough NNI search. [default: False]" name="pallnni" selected="False" type="boolean"/> 386 <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" />
389 <param label="--p-fast: --p-no-fast Fast search to resemble FastTree. [default: False]" name="pfast" selected="False" type="boolean"/> 387 <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" />
390 <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. [optional]" name="palrt" optional="True" type="integer" min="1000"/> 388 <param label="--p-n-iter: INTEGER Fix number of iterations to stop. If not set, Range(1, None) program defaults will be used. See IQ-TREE manual for details. [optional]" name="pniter" optional="False" type="text" />
391 <param label="--p-abayes: --p-no-abayes Single branch test method. Approximate Bayes test. Can be used with other 'single branch test methods'. Values reported in the order of: alrt, lbp, abayes. [default: False]" name="pabayes" selected="False" type="boolean"/> 389 <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" />
392 <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. [optional]" name="plbp" optional="True" type="integer" min="1000"/> 390 <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" />
393 <param label="--p-safe: --p-no-safe Safe likelihood kernel to avoid numerical underflow. [default: False]" name="psafe" selected="False" type="boolean"/> 391 <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" />
394 </inputs> 392 <param label="--p-allnni: --p-allnni: / --p-no-allnni Perform more thorough NNI search. [default: False]" name="pallnni" selected="False" type="boolean" />
395 <outputs> 393 <param label="--p-fast: --p-fast: / --p-no-fast Fast search to resemble FastTree. [default: False]" name="pfast" selected="False" type="boolean" />
396 <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree"/> 394 <param label="--p-alrt: INTEGER Single branch test method. Number of bootstrap Range(1000, None) replicates to perform an SH-like approximate likelihood ratio test (SH-aLRT). Minimum of 1000 replicates is recomended. Can be used with other \'single branch test methods\'. Values reported in the order of: alrt, lbp, abayes. [optional]" name="palrt" optional="False" type="text" />
397 </outputs> 395 <param label="--p-abayes: --p-abayes: / --p-no-abayes Single branch test method. Approximate Bayes test. Can be used with other \'single branch test methods\'. Values reported in the order of: alrt, lbp, abayes. [default: False]" name="pabayes" selected="False" type="boolean" />
398 <help><![CDATA[ 396 <param label="--p-lbp: INTEGER Single branch test method. Number of bootstrap Range(1000, None) replicates to perform a fast local bootstrap probability method. Minimum of 1000 replicates is recomended. Can be used with other \'single branch test methods\'. Values reported in the order of: alrt, lbp, abayes. [optional]" name="plbp" optional="False" type="text" />
397 <param label="--p-safe: --p-safe: / --p-no-safe Safe likelihood kernel to avoid numerical underflow. [default: False]" name="psafe" selected="False" type="boolean" />
398 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
399
400 </inputs>
401
402 <outputs>
403 <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree" />
404
405 </outputs>
406
407 <help><![CDATA[
399 Construct a phylogenetic tree with IQ-TREE. 408 Construct a phylogenetic tree with IQ-TREE.
400 ########################################### 409 ###############################################################
401 410
402 Construct a phylogenetic tree using IQ-TREE (http://www.iqtree.org/) with 411 Construct a phylogenetic tree using IQ-TREE (http://www.iqtree.org/) with
403 automatic model selection. 412 automatic model selection.
404 413
405 Parameters 414 Parameters
407 alignment : FeatureData[AlignedSequence] 416 alignment : FeatureData[AlignedSequence]
408 Aligned sequences to be used for phylogenetic reconstruction. 417 Aligned sequences to be used for phylogenetic reconstruction.
409 seed : Int, optional 418 seed : Int, optional
410 Random number seed. If not set, program defaults will be used. See IQ- 419 Random number seed. If not set, program defaults will be used. See IQ-
411 TREE manual for details. 420 TREE manual for details.
421 n_cores : Int % Range(1, None) | Str % Choices('auto'), optional
422 The number of cores to use for parallel processing. Use `auto` to let
423 IQ-TREE automatically determine the optimal number of cores to use.
424 n_cores_max : Int % Range(2, None), optional
425 Limits the maximum number of cores to be used when 'n_cores' is set to
426 'auto'.
412 n_runs : Int % Range(1, None), optional 427 n_runs : Int % Range(1, None), optional
413 Number of indepedent runs. Multiple independent runs (e.g. 10) can 428 Number of indepedent runs. Multiple independent runs (e.g. 10) can
414 outperform a single run in terms of likelihood maximisation. 429 outperform a single run in terms of likelihood maximisation.
415 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 430 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
416 Model of Nucleotide Substitution. If not provided, IQ-TREE will 431 Model of Nucleotide Substitution. If not provided, IQ-TREE will
428 Fix number of iterations to stop. If not set, program defaults will be 443 Fix number of iterations to stop. If not set, program defaults will be
429 used. See IQ-TREE manual for details. 444 used. See IQ-TREE manual for details.
430 stop_iter : Int % Range(1, None), optional 445 stop_iter : Int % Range(1, None), optional
431 Number of unsuccessful iterations to stop. If not set, program defaults 446 Number of unsuccessful iterations to stop. If not set, program defaults
432 will be used. See IQ-TREE manual for details. 447 will be used. See IQ-TREE manual for details.
433 perturb_nni_strength : Float % Range(0.01, 99), optional 448 perturb_nni_strength : Float % Range(0.01, 1.0), optional
434 Perturbation strength for randomized NNI. If not set, program defaults 449 Perturbation strength for randomized NNI. If not set, program defaults
435 will be used. See IQ-TREE manual for details. 450 will be used. See IQ-TREE manual for details.
436 spr_radius : Int % Range(1, None), optional 451 spr_radius : Int % Range(1, None), optional
437 Radius for parsimony SPR search. If not set, program defaults will be 452 Radius for parsimony SPR search. If not set, program defaults will be
438 used. See IQ-TREE manual for details. 453 used. See IQ-TREE manual for details.
441 fast : Bool, optional 456 fast : Bool, optional
442 Fast search to resemble FastTree. 457 Fast search to resemble FastTree.
443 alrt : Int % Range(1000, None), optional 458 alrt : Int % Range(1000, None), optional
444 Single branch test method. Number of bootstrap replicates to perform an 459 Single branch test method. Number of bootstrap replicates to perform an
445 SH-like approximate likelihood ratio test (SH-aLRT). Minimum of 1000 460 SH-like approximate likelihood ratio test (SH-aLRT). Minimum of 1000
446 replicates is recomended. Set to '0' for parametric aLRT test. Can be 461 replicates is recomended. Can be used with other 'single branch test
447 used with other 'single branch test methods'. Values reported in the 462 methods'. Values reported in the order of: alrt, lbp, abayes.
448 order of: alrt, lbp, abayes.
449 abayes : Bool, optional 463 abayes : Bool, optional
450 Single branch test method. Approximate Bayes test. Can be used with 464 Single branch test method. Approximate Bayes test. Can be used with
451 other 'single branch test methods'. Values reported in the order of: 465 other 'single branch test methods'. Values reported in the order of:
452 alrt, lbp, abayes. 466 alrt, lbp, abayes.
453 lbp : Int % Range(1000, None), optional 467 lbp : Int % Range(1000, None), optional
460 474
461 Returns 475 Returns
462 ------- 476 -------
463 tree : Phylogeny[Unrooted] 477 tree : Phylogeny[Unrooted]
464 The resulting phylogenetic tree. 478 The resulting phylogenetic tree.
465 ]]></help> 479 ]]></help>
466 <macros> 480 <macros>
467 <import>qiime_citation.xml</import> 481 <import>qiime_citation.xml</import>
468 </macros> 482 </macros>
469 <expand macro="qiime_citation"/> 483 <expand macro="qiime_citation"/>
470 </tool> 484 </tool>