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comparison qiime2/qiime_phylogeny_iqtree.xml @ 0:370e0b6e9826 draft

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_phylogeny_iqtree" name="qiime phylogeny iqtree" version="2019.4">
3 <description> - Construct a phylogenetic tree with IQ-TREE.</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime phylogeny iqtree
9
10 --i-alignment=$ialignment
11
12 #if str($pseed):
13 --p-seed="$pseed"
14 #end if
15
16 #set $pncores = '${GALAXY_SLOTS:-4}'
17
18 #if str($pncores):
19 --p-n-cores="$pncores"
20 #end if
21
22 #if $pnruns:
23 --p-n-runs=$pnruns
24 #end if
25
26 #if str($psubstitutionmodel) != 'None':
27 --p-substitution-model=$psubstitutionmodel
28 #end if
29
30 #if str($pninitparstrees):
31 --p-n-init-pars-trees="$pninitparstrees"
32 #end if
33
34 #if str($pntopinittrees):
35 --p-n-top-init-trees="$pntopinittrees"
36 #end if
37
38 #if str($pnbestretaintrees):
39 --p-n-best-retain-trees="$pnbestretaintrees"
40 #end if
41
42 #if str($pniter):
43 --p-n-iter="$pniter"
44 #end if
45
46 #if str($pstopiter):
47 --p-stop-iter="$pstopiter"
48 #end if
49
50 #if str($pperturbnnistrength):
51 --p-perturb-nni-strength="$pperturbnnistrength"
52 #end if
53
54 #if str($psprradius):
55 --p-spr-radius="$psprradius"
56 #end if
57
58 #if $pallnni:
59 --p-allnni
60 #end if
61
62 #if $pfast:
63 --p-fast
64 #end if
65
66 #if str($palrt):
67 --p-alrt="$palrt"
68 #end if
69
70 #if $pabayes:
71 --p-abayes
72 #end if
73
74 #if str($plbp):
75 --p-lbp="$plbp"
76 #end if
77
78 #if $psafe:
79 --p-safe
80 #end if
81
82 --o-tree=otree
83 ;
84 cp otree.qza $otree
85 ]]></command>
86 <inputs>
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"/>
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"/>
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"/>
90 <param label="--p-substitution-model: " name="psubstitutionmodel" optional="True" type="select">
91 <option selected="True" value="None">Selection is Optional</option>
92 <option value="JC">JC</option>
93 <option value="JC+I">JC+I</option>
94 <option value="JC+G">JC+G</option>
95 <option value="JC+I+G">JC+I+G</option>
96 <option value="JC+R2">JC+R2</option>
97 <option value="JC+R3">JC+R3</option>
98 <option value="JC+R4">JC+R4</option>
99 <option value="JC+R5">JC+R5</option>
100 <option value="JC+R6">JC+R6</option>
101 <option value="JC+R7">JC+R7</option>
102 <option value="JC+R8">JC+R8</option>
103 <option value="JC+R9">JC+R9</option>
104 <option value="JC+R10">JC+R10</option>
105 <option value="F81">F81</option>
106 <option value="F81+I">F81+I</option>
107 <option value="F81+G">F81+G</option>
108 <option value="F81+I+G">F81+I+G</option>
109 <option value="F81+R2">F81+R2</option>
110 <option value="F81+R3">F81+R3</option>
111 <option value="F81+R4">F81+R4</option>
112 <option value="F81+R5">F81+R5</option>
113 <option value="F81+R6">F81+R6</option>
114 <option value="F81+R7">F81+R7</option>
115 <option value="F81+R8">F81+R8</option>
116 <option value="F81+R9">F81+R9</option>
117 <option value="F81+R10">F81+R10</option>
118 <option value="K80">K80</option>
119 <option value="K80+I">K80+I</option>
120 <option value="K80+G">K80+G</option>
121 <option value="K80+I+G">K80+I+G</option>
122 <option value="K80+R2">K80+R2</option>
123 <option value="K80+R3">K80+R3</option>
124 <option value="K80+R4">K80+R4</option>
125 <option value="K80+R5">K80+R5</option>
126 <option value="K80+R6">K80+R6</option>
127 <option value="K80+R7">K80+R7</option>
128 <option value="K80+R8">K80+R8</option>
129 <option value="K80+R9">K80+R9</option>
130 <option value="K80+R10">K80+R10</option>
131 <option value="HKY">HKY</option>
132 <option value="HKY+I">HKY+I</option>
133 <option value="HKY+G">HKY+G</option>
134 <option value="HKY+I+G">HKY+I+G</option>
135 <option value="HKY+R2">HKY+R2</option>
136 <option value="HKY+R3">HKY+R3</option>
137 <option value="HKY+R4">HKY+R4</option>
138 <option value="HKY+R5">HKY+R5</option>
139 <option value="HKY+R6">HKY+R6</option>
140 <option value="HKY+R7">HKY+R7</option>
141 <option value="HKY+R8">HKY+R8</option>
142 <option value="HKY+R9">HKY+R9</option>
143 <option value="HKY+R10">HKY+R10</option>
144 <option value="TNe">TNe</option>
145 <option value="TNe+I">TNe+I</option>
146 <option value="TNe+G">TNe+G</option>
147 <option value="TNe+I+G">TNe+I+G</option>
148 <option value="TNe+R2">TNe+R2</option>
149 <option value="TNe+R3">TNe+R3</option>
150 <option value="TNe+R4">TNe+R4</option>
151 <option value="TNe+R5">TNe+R5</option>
152 <option value="TNe+R6">TNe+R6</option>
153 <option value="TNe+R7">TNe+R7</option>
154 <option value="TNe+R8">TNe+R8</option>
155 <option value="TNe+R9">TNe+R9</option>
156 <option value="TNe+R10">TNe+R10</option>
157 <option value="TN">TN</option>
158 <option value="TN+I">TN+I</option>
159 <option value="TN+G">TN+G</option>
160 <option value="TN+I+G">TN+I+G</option>
161 <option value="TN+R2">TN+R2</option>
162 <option value="TN+R3">TN+R3</option>
163 <option value="TN+R4">TN+R4</option>
164 <option value="TN+R5">TN+R5</option>
165 <option value="TN+R6">TN+R6</option>
166 <option value="TN+R7">TN+R7</option>
167 <option value="TN+R8">TN+R8</option>
168 <option value="TN+R9">TN+R9</option>
169 <option value="TN+R10">TN+R10</option>
170 <option value="K81">K81</option>
171 <option value="K81+I">K81+I</option>
172 <option value="K81+G">K81+G</option>
173 <option value="K81+I+G">K81+I+G</option>
174 <option value="K81+R2">K81+R2</option>
175 <option value="K81+R3">K81+R3</option>
176 <option value="K81+R4">K81+R4</option>
177 <option value="K81+R5">K81+R5</option>
178 <option value="K81+R6">K81+R6</option>
179 <option value="K81+R7">K81+R7</option>
180 <option value="K81+R8">K81+R8</option>
181 <option value="K81+R9">K81+R9</option>
182 <option value="K81+R10">K81+R10</option>
183 <option value="K81u">K81u</option>
184 <option value="K81u+I">K81u+I</option>
185 <option value="K81u+G">K81u+G</option>
186 <option value="K81u+I+G">K81u+I+G</option>
187 <option value="K81u+R2">K81u+R2</option>
188 <option value="K81u+R3">K81u+R3</option>
189 <option value="K81u+R4">K81u+R4</option>
190 <option value="K81u+R5">K81u+R5</option>
191 <option value="K81u+R6">K81u+R6</option>
192 <option value="K81u+R7">K81u+R7</option>
193 <option value="K81u+R8">K81u+R8</option>
194 <option value="K81u+R9">K81u+R9</option>
195 <option value="K81u+R10">K81u+R10</option>
196 <option value="TPM2">TPM2</option>
197 <option value="TPM2+I">TPM2+I</option>
198 <option value="TPM2+G">TPM2+G</option>
199 <option value="TPM2+I+G">TPM2+I+G</option>
200 <option value="TPM2+R2">TPM2+R2</option>
201 <option value="TPM2+R3">TPM2+R3</option>
202 <option value="TPM2+R4">TPM2+R4</option>
203 <option value="TPM2+R5">TPM2+R5</option>
204 <option value="TPM2+R6">TPM2+R6</option>
205 <option value="TPM2+R7">TPM2+R7</option>
206 <option value="TPM2+R8">TPM2+R8</option>
207 <option value="TPM2+R9">TPM2+R9</option>
208 <option value="TPM2+R10">TPM2+R10</option>
209 <option value="TPM2u">TPM2u</option>
210 <option value="TPM2u+I">TPM2u+I</option>
211 <option value="TPM2u+G">TPM2u+G</option>
212 <option value="TPM2u+I+G">TPM2u+I+G</option>
213 <option value="TPM2u+R2">TPM2u+R2</option>
214 <option value="TPM2u+R3">TPM2u+R3</option>
215 <option value="TPM2u+R4">TPM2u+R4</option>
216 <option value="TPM2u+R5">TPM2u+R5</option>
217 <option value="TPM2u+R6">TPM2u+R6</option>
218 <option value="TPM2u+R7">TPM2u+R7</option>
219 <option value="TPM2u+R8">TPM2u+R8</option>
220 <option value="TPM2u+R9">TPM2u+R9</option>
221 <option value="TPM2u+R10">TPM2u+R10</option>
222 <option value="TPM3">TPM3</option>
223 <option value="TPM3+I">TPM3+I</option>
224 <option value="TPM3+G">TPM3+G</option>
225 <option value="TPM3+I+G">TPM3+I+G</option>
226 <option value="TPM3+R2">TPM3+R2</option>
227 <option value="TPM3+R3">TPM3+R3</option>
228 <option value="TPM3+R4">TPM3+R4</option>
229 <option value="TPM3+R5">TPM3+R5</option>
230 <option value="TPM3+R6">TPM3+R6</option>
231 <option value="TPM3+R7">TPM3+R7</option>
232 <option value="TPM3+R8">TPM3+R8</option>
233 <option value="TPM3+R9">TPM3+R9</option>
234 <option value="TPM3+R10">TPM3+R10</option>
235 <option value="TPM3u">TPM3u</option>
236 <option value="TPM3u+I">TPM3u+I</option>
237 <option value="TPM3u+G">TPM3u+G</option>
238 <option value="TPM3u+I+G">TPM3u+I+G</option>
239 <option value="TPM3u+R2">TPM3u+R2</option>
240 <option value="TPM3u+R3">TPM3u+R3</option>
241 <option value="TPM3u+R4">TPM3u+R4</option>
242 <option value="TPM3u+R5">TPM3u+R5</option>
243 <option value="TPM3u+R6">TPM3u+R6</option>
244 <option value="TPM3u+R7">TPM3u+R7</option>
245 <option value="TPM3u+R8">TPM3u+R8</option>
246 <option value="TPM3u+R9">TPM3u+R9</option>
247 <option value="TPM3u+R10">TPM3u+R10</option>
248 <option value="TIMe">TIMe</option>
249 <option value="TIMe+I">TIMe+I</option>
250 <option value="TIMe+G">TIMe+G</option>
251 <option value="TIMe+I+G">TIMe+I+G</option>
252 <option value="TIMe+R2">TIMe+R2</option>
253 <option value="TIMe+R3">TIMe+R3</option>
254 <option value="TIMe+R4">TIMe+R4</option>
255 <option value="TIMe+R5">TIMe+R5</option>
256 <option value="TIMe+R6">TIMe+R6</option>
257 <option value="TIMe+R7">TIMe+R7</option>
258 <option value="TIMe+R8">TIMe+R8</option>
259 <option value="TIMe+R9">TIMe+R9</option>
260 <option value="TIMe+R10">TIMe+R10</option>
261 <option value="TIM">TIM</option>
262 <option value="TIM+I">TIM+I</option>
263 <option value="TIM+G">TIM+G</option>
264 <option value="TIM+I+G">TIM+I+G</option>
265 <option value="TIM+R2">TIM+R2</option>
266 <option value="TIM+R3">TIM+R3</option>
267 <option value="TIM+R4">TIM+R4</option>
268 <option value="TIM+R5">TIM+R5</option>
269 <option value="TIM+R6">TIM+R6</option>
270 <option value="TIM+R7">TIM+R7</option>
271 <option value="TIM+R8">TIM+R8</option>
272 <option value="TIM+R9">TIM+R9</option>
273 <option value="TIM+R10">TIM+R10</option>
274 <option value="TIM2e">TIM2e</option>
275 <option value="TIM2e+I">TIM2e+I</option>
276 <option value="TIM2e+G">TIM2e+G</option>
277 <option value="TIM2e+I+G">TIM2e+I+G</option>
278 <option value="TIM2e+R2">TIM2e+R2</option>
279 <option value="TIM2e+R3">TIM2e+R3</option>
280 <option value="TIM2e+R4">TIM2e+R4</option>
281 <option value="TIM2e+R5">TIM2e+R5</option>
282 <option value="TIM2e+R6">TIM2e+R6</option>
283 <option value="TIM2e+R7">TIM2e+R7</option>
284 <option value="TIM2e+R8">TIM2e+R8</option>
285 <option value="TIM2e+R9">TIM2e+R9</option>
286 <option value="TIM2e+R10">TIM2e+R10</option>
287 <option value="TIM2">TIM2</option>
288 <option value="TIM2+I">TIM2+I</option>
289 <option value="TIM2+G">TIM2+G</option>
290 <option value="TIM2+I+G">TIM2+I+G</option>
291 <option value="TIM2+R2">TIM2+R2</option>
292 <option value="TIM2+R3">TIM2+R3</option>
293 <option value="TIM2+R4">TIM2+R4</option>
294 <option value="TIM2+R5">TIM2+R5</option>
295 <option value="TIM2+R6">TIM2+R6</option>
296 <option value="TIM2+R7">TIM2+R7</option>
297 <option value="TIM2+R8">TIM2+R8</option>
298 <option value="TIM2+R9">TIM2+R9</option>
299 <option value="TIM2+R10">TIM2+R10</option>
300 <option value="TIM3e">TIM3e</option>
301 <option value="TIM3e+I">TIM3e+I</option>
302 <option value="TIM3e+G">TIM3e+G</option>
303 <option value="TIM3e+I+G">TIM3e+I+G</option>
304 <option value="TIM3e+R2">TIM3e+R2</option>
305 <option value="TIM3e+R3">TIM3e+R3</option>
306 <option value="TIM3e+R4">TIM3e+R4</option>
307 <option value="TIM3e+R5">TIM3e+R5</option>
308 <option value="TIM3e+R6">TIM3e+R6</option>
309 <option value="TIM3e+R7">TIM3e+R7</option>
310 <option value="TIM3e+R8">TIM3e+R8</option>
311 <option value="TIM3e+R9">TIM3e+R9</option>
312 <option value="TIM3e+R10">TIM3e+R10</option>
313 <option value="TIM3">TIM3</option>
314 <option value="TIM3+I">TIM3+I</option>
315 <option value="TIM3+G">TIM3+G</option>
316 <option value="TIM3+I+G">TIM3+I+G</option>
317 <option value="TIM3+R2">TIM3+R2</option>
318 <option value="TIM3+R3">TIM3+R3</option>
319 <option value="TIM3+R4">TIM3+R4</option>
320 <option value="TIM3+R5">TIM3+R5</option>
321 <option value="TIM3+R6">TIM3+R6</option>
322 <option value="TIM3+R7">TIM3+R7</option>
323 <option value="TIM3+R8">TIM3+R8</option>
324 <option value="TIM3+R9">TIM3+R9</option>
325 <option value="TIM3+R10">TIM3+R10</option>
326 <option value="TVMe">TVMe</option>
327 <option value="TVMe+I">TVMe+I</option>
328 <option value="TVMe+G">TVMe+G</option>
329 <option value="TVMe+I+G">TVMe+I+G</option>
330 <option value="TVMe+R2">TVMe+R2</option>
331 <option value="TVMe+R3">TVMe+R3</option>
332 <option value="TVMe+R4">TVMe+R4</option>
333 <option value="TVMe+R5">TVMe+R5</option>
334 <option value="TVMe+R6">TVMe+R6</option>
335 <option value="TVMe+R7">TVMe+R7</option>
336 <option value="TVMe+R8">TVMe+R8</option>
337 <option value="TVMe+R9">TVMe+R9</option>
338 <option value="TVMe+R10">TVMe+R10</option>
339 <option value="TVM">TVM</option>
340 <option value="TVM+I">TVM+I</option>
341 <option value="TVM+G">TVM+G</option>
342 <option value="TVM+I+G">TVM+I+G</option>
343 <option value="TVM+R2">TVM+R2</option>
344 <option value="TVM+R3">TVM+R3</option>
345 <option value="TVM+R4">TVM+R4</option>
346 <option value="TVM+R5">TVM+R5</option>
347 <option value="TVM+R6">TVM+R6</option>
348 <option value="TVM+R7">TVM+R7</option>
349 <option value="TVM+R8">TVM+R8</option>
350 <option value="TVM+R9">TVM+R9</option>
351 <option value="TVM+R10">TVM+R10</option>
352 <option value="SYM">SYM</option>
353 <option value="SYM+I">SYM+I</option>
354 <option value="SYM+G">SYM+G</option>
355 <option value="SYM+I+G">SYM+I+G</option>
356 <option value="SYM+R2">SYM+R2</option>
357 <option value="SYM+R3">SYM+R3</option>
358 <option value="SYM+R4">SYM+R4</option>
359 <option value="SYM+R5">SYM+R5</option>
360 <option value="SYM+R6">SYM+R6</option>
361 <option value="SYM+R7">SYM+R7</option>
362 <option value="SYM+R8">SYM+R8</option>
363 <option value="SYM+R9">SYM+R9</option>
364 <option value="SYM+R10">SYM+R10</option>
365 <option value="GTR">GTR</option>
366 <option value="GTR+I">GTR+I</option>
367 <option value="GTR+G">GTR+G</option>
368 <option value="GTR+I+G">GTR+I+G</option>
369 <option value="GTR+R2">GTR+R2</option>
370 <option value="GTR+R3">GTR+R3</option>
371 <option value="GTR+R4">GTR+R4</option>
372 <option value="GTR+R5">GTR+R5</option>
373 <option value="GTR+R6">GTR+R6</option>
374 <option value="GTR+R7">GTR+R7</option>
375 <option value="GTR+R8">GTR+R8</option>
376 <option value="GTR+R9">GTR+R9</option>
377 <option value="GTR+R10">GTR+R10</option>
378 <option value="MFP">MFP</option>
379 <option value="TEST">TEST</option>
380 </param>
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"/>
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"/>
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"/>
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"/>
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"/>
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"/>
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"/>
388 <param label="--p-allnni: --p-no-allnni Perform more thorough NNI search. [default: False]" name="pallnni" selected="False" type="boolean"/>
389 <param label="--p-fast: --p-no-fast Fast search to resemble FastTree. [default: False]" name="pfast" selected="False" type="boolean"/>
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"/>
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"/>
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"/>
393 <param label="--p-safe: --p-no-safe Safe likelihood kernel to avoid numerical underflow. [default: False]" name="psafe" selected="False" type="boolean"/>
394 </inputs>
395 <outputs>
396 <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree"/>
397 </outputs>
398 <help><![CDATA[
399 Construct a phylogenetic tree with IQ-TREE.
400 ###########################################
401
402 Construct a phylogenetic tree using IQ-TREE (http://www.iqtree.org/) with
403 automatic model selection.
404
405 Parameters
406 ----------
407 alignment : FeatureData[AlignedSequence]
408 Aligned sequences to be used for phylogenetic reconstruction.
409 seed : Int, optional
410 Random number seed. If not set, program defaults will be used. See IQ-
411 TREE manual for details.
412 n_runs : Int % Range(1, None), optional
413 Number of indepedent runs. Multiple independent runs (e.g. 10) can
414 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
416 Model of Nucleotide Substitution. If not provided, IQ-TREE will
417 determine the best fit substitution model automatically.
418 n_init_pars_trees : Int % Range(1, None), optional
419 Number of initial parsimony trees. If not set, program defaults will be
420 used. See IQ-TREE manual for details.
421 n_top_init_trees : Int % Range(1, None), optional
422 Number of top initial trees. If not set, program defaults will be used.
423 See IQ-TREE manual for details.
424 n_best_retain_trees : Int % Range(1, None), optional
425 Number of best trees retained during search. If not set, program
426 defaults will be used. See IQ-TREE manual for details.
427 n_iter : Int % Range(1, None), optional
428 Fix number of iterations to stop. If not set, program defaults will be
429 used. See IQ-TREE manual for details.
430 stop_iter : Int % Range(1, None), optional
431 Number of unsuccessful iterations to stop. If not set, program defaults
432 will be used. See IQ-TREE manual for details.
433 perturb_nni_strength : Float % Range(0.01, 99), optional
434 Perturbation strength for randomized NNI. If not set, program defaults
435 will be used. See IQ-TREE manual for details.
436 spr_radius : Int % Range(1, None), optional
437 Radius for parsimony SPR search. If not set, program defaults will be
438 used. See IQ-TREE manual for details.
439 allnni : Bool, optional
440 Perform more thorough NNI search.
441 fast : Bool, optional
442 Fast search to resemble FastTree.
443 alrt : Int % Range(1000, None), optional
444 Single branch test method. Number of bootstrap replicates to perform an
445 SH-like approximate likelihood ratio test (SH-aLRT). Minimum of 1000
446 replicates is recomended. Set to '0' for parametric aLRT test. Can be
447 used with other 'single branch test methods'. Values reported in the
448 order of: alrt, lbp, abayes.
449 abayes : Bool, optional
450 Single branch test method. Approximate Bayes test. Can be used with
451 other 'single branch test methods'. Values reported in the order of:
452 alrt, lbp, abayes.
453 lbp : Int % Range(1000, None), optional
454 Single branch test method. Number of bootstrap replicates to perform a
455 fast local bootstrap probability method. Minimum of 1000 replicates is
456 recomended. Can be used with other 'single branch test methods'. Values
457 reported in the order of: alrt, lbp, abayes.
458 safe : Bool, optional
459 Safe likelihood kernel to avoid numerical underflow.
460
461 Returns
462 -------
463 tree : Phylogeny[Unrooted]
464 The resulting phylogenetic tree.
465 ]]></help>
466 <macros>
467 <import>qiime_citation.xml</import>
468 </macros>
469 <expand macro="qiime_citation"/>
470 </tool>