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comparison qiime2-2020.8/qiime_phylogeny_iqtree.xml @ 0:5c352d975ef7 draft

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author florianbegusch
date Thu, 03 Sep 2020 09:33:04 +0000
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1 <?xml version="1.0" ?>
2 <tool id="qiime_phylogeny_iqtree" name="qiime phylogeny iqtree"
3 version="2020.8">
4 <description>Construct a phylogenetic tree with IQ-TREE.</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime phylogeny iqtree
10
11 --i-alignment=$ialignment
12
13 #if str($pseed):
14 --p-seed=$pseed
15 #end if
16 #if str($pncores) != 'None':
17 --p-n-cores=$pncores
18 #end if
19
20 #set $pncoresmax = '${GALAXY_SLOTS:-4}'
21
22 #if str($pncoresmax):
23 --p-n-cores-max=$pncoresmax
24 #end if
25
26 --p-n-runs=$pnruns
27
28 #if str($psubstitutionmodel) != 'None':
29 --p-substitution-model=$psubstitutionmodel
30 #end if
31
32 #if str($pninitparstrees):
33 --p-n-init-pars-trees=$pninitparstrees
34 #end if
35 #if str($pntopinittrees):
36 --p-n-top-init-trees=$pntopinittrees
37 #end if
38 #if str($pnbestretaintrees):
39 --p-n-best-retain-trees=$pnbestretaintrees
40 #end if
41 #if str($pniter):
42 --p-n-iter=$pniter
43 #end if
44 #if str($pstopiter):
45 --p-stop-iter=$pstopiter
46 #end if
47 #if str($pperturbnnistrength):
48 --p-perturb-nni-strength=$pperturbnnistrength
49 #end if
50 #if str($psprradius):
51 --p-spr-radius=$psprradius
52 #end if
53 #if $pallnni:
54 --p-allnni
55 #end if
56
57 #if $pfast:
58 --p-fast
59 #end if
60
61 #if str($palrt):
62 --p-alrt=$palrt
63 #end if
64 #if $pabayes:
65 --p-abayes
66 #end if
67
68 #if str($plbp):
69 --p-lbp=$plbp
70 #end if
71 #if $psafe:
72 --p-safe
73 #end if
74
75 --o-tree=otree
76
77 #if str($examples) != 'None':
78 --examples=$examples
79 #end if
80
81 ;
82 cp otree.qza $otree
83
84 ]]></command>
85 <inputs>
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" />
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" />
88 <param label="--p-n-cores: " name="pncores" optional="True" type="select">
89 <option selected="True" value="None">Selection is Optional</option>
90 <option value="Int % Range(1">Int % Range(1</option>
91 <option value="None">None</option>
92 </param>
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" />
94 <param label="--p-substitution-model: " name="psubstitutionmodel" optional="True" type="select">
95 <option selected="True" value="None">Selection is Optional</option>
96 <option value="JC">JC</option>
97 <option value="JC+I">JC+I</option>
98 <option value="JC+G">JC+G</option>
99 <option value="JC+I+G">JC+I+G</option>
100 <option value="JC+R2">JC+R2</option>
101 <option value="JC+R3">JC+R3</option>
102 <option value="JC+R4">JC+R4</option>
103 <option value="JC+R5">JC+R5</option>
104 <option value="JC+R6">JC+R6</option>
105 <option value="JC+R7">JC+R7</option>
106 <option value="JC+R8">JC+R8</option>
107 <option value="JC+R9">JC+R9</option>
108 <option value="JC+R10">JC+R10</option>
109 <option value="F81">F81</option>
110 <option value="F81+I">F81+I</option>
111 <option value="F81+G">F81+G</option>
112 <option value="F81+I+G">F81+I+G</option>
113 <option value="F81+R2">F81+R2</option>
114 <option value="F81+R3">F81+R3</option>
115 <option value="F81+R4">F81+R4</option>
116 <option value="F81+R5">F81+R5</option>
117 <option value="F81+R6">F81+R6</option>
118 <option value="F81+R7">F81+R7</option>
119 <option value="F81+R8">F81+R8</option>
120 <option value="F81+R9">F81+R9</option>
121 <option value="F81+R10">F81+R10</option>
122 <option value="K80">K80</option>
123 <option value="K80+I">K80+I</option>
124 <option value="K80+G">K80+G</option>
125 <option value="K80+I+G">K80+I+G</option>
126 <option value="K80+R2">K80+R2</option>
127 <option value="K80+R3">K80+R3</option>
128 <option value="K80+R4">K80+R4</option>
129 <option value="K80+R5">K80+R5</option>
130 <option value="K80+R6">K80+R6</option>
131 <option value="K80+R7">K80+R7</option>
132 <option value="K80+R8">K80+R8</option>
133 <option value="K80+R9">K80+R9</option>
134 <option value="K80+R10">K80+R10</option>
135 <option value="HKY">HKY</option>
136 <option value="HKY+I">HKY+I</option>
137 <option value="HKY+G">HKY+G</option>
138 <option value="HKY+I+G">HKY+I+G</option>
139 <option value="HKY+R2">HKY+R2</option>
140 <option value="HKY+R3">HKY+R3</option>
141 <option value="HKY+R4">HKY+R4</option>
142 <option value="HKY+R5">HKY+R5</option>
143 <option value="HKY+R6">HKY+R6</option>
144 <option value="HKY+R7">HKY+R7</option>
145 <option value="HKY+R8">HKY+R8</option>
146 <option value="HKY+R9">HKY+R9</option>
147 <option value="HKY+R10">HKY+R10</option>
148 <option value="TNe">TNe</option>
149 <option value="TNe+I">TNe+I</option>
150 <option value="TNe+G">TNe+G</option>
151 <option value="TNe+I+G">TNe+I+G</option>
152 <option value="TNe+R2">TNe+R2</option>
153 <option value="TNe+R3">TNe+R3</option>
154 <option value="TNe+R4">TNe+R4</option>
155 <option value="TNe+R5">TNe+R5</option>
156 <option value="TNe+R6">TNe+R6</option>
157 <option value="TNe+R7">TNe+R7</option>
158 <option value="TNe+R8">TNe+R8</option>
159 <option value="TNe+R9">TNe+R9</option>
160 <option value="TNe+R10">TNe+R10</option>
161 <option value="TN">TN</option>
162 <option value="TN+I">TN+I</option>
163 <option value="TN+G">TN+G</option>
164 <option value="TN+I+G">TN+I+G</option>
165 <option value="TN+R2">TN+R2</option>
166 <option value="TN+R3">TN+R3</option>
167 <option value="TN+R4">TN+R4</option>
168 <option value="TN+R5">TN+R5</option>
169 <option value="TN+R6">TN+R6</option>
170 <option value="TN+R7">TN+R7</option>
171 <option value="TN+R8">TN+R8</option>
172 <option value="TN+R9">TN+R9</option>
173 <option value="TN+R10">TN+R10</option>
174 <option value="K81">K81</option>
175 <option value="K81+I">K81+I</option>
176 <option value="K81+G">K81+G</option>
177 <option value="K81+I+G">K81+I+G</option>
178 <option value="K81+R2">K81+R2</option>
179 <option value="K81+R3">K81+R3</option>
180 <option value="K81+R4">K81+R4</option>
181 <option value="K81+R5">K81+R5</option>
182 <option value="K81+R6">K81+R6</option>
183 <option value="K81+R7">K81+R7</option>
184 <option value="K81+R8">K81+R8</option>
185 <option value="K81+R9">K81+R9</option>
186 <option value="K81+R10">K81+R10</option>
187 <option value="K81u">K81u</option>
188 <option value="K81u+I">K81u+I</option>
189 <option value="K81u+G">K81u+G</option>
190 <option value="K81u+I+G">K81u+I+G</option>
191 <option value="K81u+R2">K81u+R2</option>
192 <option value="K81u+R3">K81u+R3</option>
193 <option value="K81u+R4">K81u+R4</option>
194 <option value="K81u+R5">K81u+R5</option>
195 <option value="K81u+R6">K81u+R6</option>
196 <option value="K81u+R7">K81u+R7</option>
197 <option value="K81u+R8">K81u+R8</option>
198 <option value="K81u+R9">K81u+R9</option>
199 <option value="K81u+R10">K81u+R10</option>
200 <option value="TPM2">TPM2</option>
201 <option value="TPM2+I">TPM2+I</option>
202 <option value="TPM2+G">TPM2+G</option>
203 <option value="TPM2+I+G">TPM2+I+G</option>
204 <option value="TPM2+R2">TPM2+R2</option>
205 <option value="TPM2+R3">TPM2+R3</option>
206 <option value="TPM2+R4">TPM2+R4</option>
207 <option value="TPM2+R5">TPM2+R5</option>
208 <option value="TPM2+R6">TPM2+R6</option>
209 <option value="TPM2+R7">TPM2+R7</option>
210 <option value="TPM2+R8">TPM2+R8</option>
211 <option value="TPM2+R9">TPM2+R9</option>
212 <option value="TPM2+R10">TPM2+R10</option>
213 <option value="TPM2u">TPM2u</option>
214 <option value="TPM2u+I">TPM2u+I</option>
215 <option value="TPM2u+G">TPM2u+G</option>
216 <option value="TPM2u+I+G">TPM2u+I+G</option>
217 <option value="TPM2u+R2">TPM2u+R2</option>
218 <option value="TPM2u+R3">TPM2u+R3</option>
219 <option value="TPM2u+R4">TPM2u+R4</option>
220 <option value="TPM2u+R5">TPM2u+R5</option>
221 <option value="TPM2u+R6">TPM2u+R6</option>
222 <option value="TPM2u+R7">TPM2u+R7</option>
223 <option value="TPM2u+R8">TPM2u+R8</option>
224 <option value="TPM2u+R9">TPM2u+R9</option>
225 <option value="TPM2u+R10">TPM2u+R10</option>
226 <option value="TPM3">TPM3</option>
227 <option value="TPM3+I">TPM3+I</option>
228 <option value="TPM3+G">TPM3+G</option>
229 <option value="TPM3+I+G">TPM3+I+G</option>
230 <option value="TPM3+R2">TPM3+R2</option>
231 <option value="TPM3+R3">TPM3+R3</option>
232 <option value="TPM3+R4">TPM3+R4</option>
233 <option value="TPM3+R5">TPM3+R5</option>
234 <option value="TPM3+R6">TPM3+R6</option>
235 <option value="TPM3+R7">TPM3+R7</option>
236 <option value="TPM3+R8">TPM3+R8</option>
237 <option value="TPM3+R9">TPM3+R9</option>
238 <option value="TPM3+R10">TPM3+R10</option>
239 <option value="TPM3u">TPM3u</option>
240 <option value="TPM3u+I">TPM3u+I</option>
241 <option value="TPM3u+G">TPM3u+G</option>
242 <option value="TPM3u+I+G">TPM3u+I+G</option>
243 <option value="TPM3u+R2">TPM3u+R2</option>
244 <option value="TPM3u+R3">TPM3u+R3</option>
245 <option value="TPM3u+R4">TPM3u+R4</option>
246 <option value="TPM3u+R5">TPM3u+R5</option>
247 <option value="TPM3u+R6">TPM3u+R6</option>
248 <option value="TPM3u+R7">TPM3u+R7</option>
249 <option value="TPM3u+R8">TPM3u+R8</option>
250 <option value="TPM3u+R9">TPM3u+R9</option>
251 <option value="TPM3u+R10">TPM3u+R10</option>
252 <option value="TIMe">TIMe</option>
253 <option value="TIMe+I">TIMe+I</option>
254 <option value="TIMe+G">TIMe+G</option>
255 <option value="TIMe+I+G">TIMe+I+G</option>
256 <option value="TIMe+R2">TIMe+R2</option>
257 <option value="TIMe+R3">TIMe+R3</option>
258 <option value="TIMe+R4">TIMe+R4</option>
259 <option value="TIMe+R5">TIMe+R5</option>
260 <option value="TIMe+R6">TIMe+R6</option>
261 <option value="TIMe+R7">TIMe+R7</option>
262 <option value="TIMe+R8">TIMe+R8</option>
263 <option value="TIMe+R9">TIMe+R9</option>
264 <option value="TIMe+R10">TIMe+R10</option>
265 <option value="TIM">TIM</option>
266 <option value="TIM+I">TIM+I</option>
267 <option value="TIM+G">TIM+G</option>
268 <option value="TIM+I+G">TIM+I+G</option>
269 <option value="TIM+R2">TIM+R2</option>
270 <option value="TIM+R3">TIM+R3</option>
271 <option value="TIM+R4">TIM+R4</option>
272 <option value="TIM+R5">TIM+R5</option>
273 <option value="TIM+R6">TIM+R6</option>
274 <option value="TIM+R7">TIM+R7</option>
275 <option value="TIM+R8">TIM+R8</option>
276 <option value="TIM+R9">TIM+R9</option>
277 <option value="TIM+R10">TIM+R10</option>
278 <option value="TIM2e">TIM2e</option>
279 <option value="TIM2e+I">TIM2e+I</option>
280 <option value="TIM2e+G">TIM2e+G</option>
281 <option value="TIM2e+I+G">TIM2e+I+G</option>
282 <option value="TIM2e+R2">TIM2e+R2</option>
283 <option value="TIM2e+R3">TIM2e+R3</option>
284 <option value="TIM2e+R4">TIM2e+R4</option>
285 <option value="TIM2e+R5">TIM2e+R5</option>
286 <option value="TIM2e+R6">TIM2e+R6</option>
287 <option value="TIM2e+R7">TIM2e+R7</option>
288 <option value="TIM2e+R8">TIM2e+R8</option>
289 <option value="TIM2e+R9">TIM2e+R9</option>
290 <option value="TIM2e+R10">TIM2e+R10</option>
291 <option value="TIM2">TIM2</option>
292 <option value="TIM2+I">TIM2+I</option>
293 <option value="TIM2+G">TIM2+G</option>
294 <option value="TIM2+I+G">TIM2+I+G</option>
295 <option value="TIM2+R2">TIM2+R2</option>
296 <option value="TIM2+R3">TIM2+R3</option>
297 <option value="TIM2+R4">TIM2+R4</option>
298 <option value="TIM2+R5">TIM2+R5</option>
299 <option value="TIM2+R6">TIM2+R6</option>
300 <option value="TIM2+R7">TIM2+R7</option>
301 <option value="TIM2+R8">TIM2+R8</option>
302 <option value="TIM2+R9">TIM2+R9</option>
303 <option value="TIM2+R10">TIM2+R10</option>
304 <option value="TIM3e">TIM3e</option>
305 <option value="TIM3e+I">TIM3e+I</option>
306 <option value="TIM3e+G">TIM3e+G</option>
307 <option value="TIM3e+I+G">TIM3e+I+G</option>
308 <option value="TIM3e+R2">TIM3e+R2</option>
309 <option value="TIM3e+R3">TIM3e+R3</option>
310 <option value="TIM3e+R4">TIM3e+R4</option>
311 <option value="TIM3e+R5">TIM3e+R5</option>
312 <option value="TIM3e+R6">TIM3e+R6</option>
313 <option value="TIM3e+R7">TIM3e+R7</option>
314 <option value="TIM3e+R8">TIM3e+R8</option>
315 <option value="TIM3e+R9">TIM3e+R9</option>
316 <option value="TIM3e+R10">TIM3e+R10</option>
317 <option value="TIM3">TIM3</option>
318 <option value="TIM3+I">TIM3+I</option>
319 <option value="TIM3+G">TIM3+G</option>
320 <option value="TIM3+I+G">TIM3+I+G</option>
321 <option value="TIM3+R2">TIM3+R2</option>
322 <option value="TIM3+R3">TIM3+R3</option>
323 <option value="TIM3+R4">TIM3+R4</option>
324 <option value="TIM3+R5">TIM3+R5</option>
325 <option value="TIM3+R6">TIM3+R6</option>
326 <option value="TIM3+R7">TIM3+R7</option>
327 <option value="TIM3+R8">TIM3+R8</option>
328 <option value="TIM3+R9">TIM3+R9</option>
329 <option value="TIM3+R10">TIM3+R10</option>
330 <option value="TVMe">TVMe</option>
331 <option value="TVMe+I">TVMe+I</option>
332 <option value="TVMe+G">TVMe+G</option>
333 <option value="TVMe+I+G">TVMe+I+G</option>
334 <option value="TVMe+R2">TVMe+R2</option>
335 <option value="TVMe+R3">TVMe+R3</option>
336 <option value="TVMe+R4">TVMe+R4</option>
337 <option value="TVMe+R5">TVMe+R5</option>
338 <option value="TVMe+R6">TVMe+R6</option>
339 <option value="TVMe+R7">TVMe+R7</option>
340 <option value="TVMe+R8">TVMe+R8</option>
341 <option value="TVMe+R9">TVMe+R9</option>
342 <option value="TVMe+R10">TVMe+R10</option>
343 <option value="TVM">TVM</option>
344 <option value="TVM+I">TVM+I</option>
345 <option value="TVM+G">TVM+G</option>
346 <option value="TVM+I+G">TVM+I+G</option>
347 <option value="TVM+R2">TVM+R2</option>
348 <option value="TVM+R3">TVM+R3</option>
349 <option value="TVM+R4">TVM+R4</option>
350 <option value="TVM+R5">TVM+R5</option>
351 <option value="TVM+R6">TVM+R6</option>
352 <option value="TVM+R7">TVM+R7</option>
353 <option value="TVM+R8">TVM+R8</option>
354 <option value="TVM+R9">TVM+R9</option>
355 <option value="TVM+R10">TVM+R10</option>
356 <option value="SYM">SYM</option>
357 <option value="SYM+I">SYM+I</option>
358 <option value="SYM+G">SYM+G</option>
359 <option value="SYM+I+G">SYM+I+G</option>
360 <option value="SYM+R2">SYM+R2</option>
361 <option value="SYM+R3">SYM+R3</option>
362 <option value="SYM+R4">SYM+R4</option>
363 <option value="SYM+R5">SYM+R5</option>
364 <option value="SYM+R6">SYM+R6</option>
365 <option value="SYM+R7">SYM+R7</option>
366 <option value="SYM+R8">SYM+R8</option>
367 <option value="SYM+R9">SYM+R9</option>
368 <option value="SYM+R10">SYM+R10</option>
369 <option value="GTR">GTR</option>
370 <option value="GTR+I">GTR+I</option>
371 <option value="GTR+G">GTR+G</option>
372 <option value="GTR+I+G">GTR+I+G</option>
373 <option value="GTR+R2">GTR+R2</option>
374 <option value="GTR+R3">GTR+R3</option>
375 <option value="GTR+R4">GTR+R4</option>
376 <option value="GTR+R5">GTR+R5</option>
377 <option value="GTR+R6">GTR+R6</option>
378 <option value="GTR+R7">GTR+R7</option>
379 <option value="GTR+R8">GTR+R8</option>
380 <option value="GTR+R9">GTR+R9</option>
381 <option value="GTR+R10">GTR+R10</option>
382 <option value="MFP">MFP</option>
383 <option value="TEST">TEST</option>
384 </param>
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" />
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" />
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" />
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" />
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" />
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" />
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" />
392 <param label="--p-allnni: --p-allnni: / --p-no-allnni Perform more thorough NNI search. [default: False]" name="pallnni" selected="False" type="boolean" />
393 <param label="--p-fast: --p-fast: / --p-no-fast Fast search to resemble FastTree. [default: False]" name="pfast" selected="False" type="boolean" />
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" />
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" />
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[
408 Construct a phylogenetic tree with IQ-TREE.
409 ###############################################################
410
411 Construct a phylogenetic tree using IQ-TREE (http://www.iqtree.org/) with
412 automatic model selection.
413
414 Parameters
415 ----------
416 alignment : FeatureData[AlignedSequence]
417 Aligned sequences to be used for phylogenetic reconstruction.
418 seed : Int, optional
419 Random number seed. If not set, program defaults will be used. See IQ-
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'.
427 n_runs : Int % Range(1, None), optional
428 Number of indepedent runs. Multiple independent runs (e.g. 10) can
429 outperform a single run in terms of likelihood maximisation.
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
431 Model of Nucleotide Substitution. If not provided, IQ-TREE will
432 determine the best fit substitution model automatically.
433 n_init_pars_trees : Int % Range(1, None), optional
434 Number of initial parsimony trees. If not set, program defaults will be
435 used. See IQ-TREE manual for details.
436 n_top_init_trees : Int % Range(1, None), optional
437 Number of top initial trees. If not set, program defaults will be used.
438 See IQ-TREE manual for details.
439 n_best_retain_trees : Int % Range(1, None), optional
440 Number of best trees retained during search. If not set, program
441 defaults will be used. See IQ-TREE manual for details.
442 n_iter : Int % Range(1, None), optional
443 Fix number of iterations to stop. If not set, program defaults will be
444 used. See IQ-TREE manual for details.
445 stop_iter : Int % Range(1, None), optional
446 Number of unsuccessful iterations to stop. If not set, program defaults
447 will be used. See IQ-TREE manual for details.
448 perturb_nni_strength : Float % Range(0.01, 1.0), optional
449 Perturbation strength for randomized NNI. If not set, program defaults
450 will be used. See IQ-TREE manual for details.
451 spr_radius : Int % Range(1, None), optional
452 Radius for parsimony SPR search. If not set, program defaults will be
453 used. See IQ-TREE manual for details.
454 allnni : Bool, optional
455 Perform more thorough NNI search.
456 fast : Bool, optional
457 Fast search to resemble FastTree.
458 alrt : Int % Range(1000, None), optional
459 Single branch test method. Number of bootstrap replicates to perform an
460 SH-like approximate likelihood ratio test (SH-aLRT). Minimum of 1000
461 replicates is recomended. Can be used with other 'single branch test
462 methods'. Values reported in the order of: alrt, lbp, abayes.
463 abayes : Bool, optional
464 Single branch test method. Approximate Bayes test. Can be used with
465 other 'single branch test methods'. Values reported in the order of:
466 alrt, lbp, abayes.
467 lbp : Int % Range(1000, None), optional
468 Single branch test method. Number of bootstrap replicates to perform a
469 fast local bootstrap probability method. Minimum of 1000 replicates is
470 recomended. Can be used with other 'single branch test methods'. Values
471 reported in the order of: alrt, lbp, abayes.
472 safe : Bool, optional
473 Safe likelihood kernel to avoid numerical underflow.
474
475 Returns
476 -------
477 tree : Phylogeny[Unrooted]
478 The resulting phylogenetic tree.
479 ]]></help>
480 <macros>
481 <import>qiime_citation.xml</import>
482 </macros>
483 <expand macro="qiime_citation"/>
484 </tool>