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comparison qiime2/qiime_phylogeny_iqtree-ultrafast-bootstrap.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-ultrafast-bootstrap" name="qiime phylogeny iqtree-ultrafast-bootstrap" version="2019.4">
3 <description> - Construct a phylogenetic tree with IQ-TREE with bootstrap supports.</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime phylogeny iqtree-ultrafast-bootstrap
9
10 --i-alignment=$ialignment
11
12 #if str($pseed):
13 --p-seed="$pseed"
14 #end if
15
16 #if $pncores:
17 --p-n-cores=$pncores
18 #end if
19
20 #if $pnruns:
21 --p-n-runs=$pnruns
22 #end if
23
24 #if str($psubstitutionmodel) != 'None':
25 --p-substitution-model=$psubstitutionmodel
26 #end if
27
28 #if $pbootstrapreplicates:
29 --p-bootstrap-replicates=$pbootstrapreplicates
30 #end if
31
32 #if str($pninitparstrees):
33 --p-n-init-pars-trees="$pninitparstrees"
34 #end if
35
36 #if str($pntopinittrees):
37 --p-n-top-init-trees="$pntopinittrees"
38 #end if
39
40 #if str($pnbestretaintrees):
41 --p-n-best-retain-trees="$pnbestretaintrees"
42 #end if
43
44 #if str($pstopiter):
45 --p-stop-iter="$pstopiter"
46 #end if
47
48 #if str($pperturbnnistrength):
49 --p-perturb-nni-strength="$pperturbnnistrength"
50 #end if
51
52 #if str($psprradius):
53 --p-spr-radius="$psprradius"
54 #end if
55
56 #if str($pnmaxufbootiter):
57 --p-n-max-ufboot-iter="$pnmaxufbootiter"
58 #end if
59
60 #if str($pnufbootsteps):
61 --p-n-ufboot-steps="$pnufbootsteps"
62 #end if
63
64 #if str($pmincorufboot):
65 --p-min-cor-ufboot="$pmincorufboot"
66 #end if
67
68 #if str($pepbreakufboot):
69 --p-ep-break-ufboot="$pepbreakufboot"
70 #end if
71
72 #if $pallnni:
73 --p-allnni
74 #end if
75
76 #if str($palrt):
77 --p-alrt="$palrt"
78 #end if
79
80 #if $pabayes:
81 --p-abayes
82 #end if
83
84 #if str($plbp):
85 --p-lbp="$plbp"
86 #end if
87
88 #if $pbnni:
89 --p-bnni
90 #end if
91
92 #if $psafe:
93 --p-safe
94 #end if
95
96 --o-tree=otree
97 ;
98 cp otree.qza $otree
99 ]]></command>
100 <inputs>
101 <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"/>
102 <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"/>
103 <param label="--p-n-cores: INTEGER The number of cores to use for parallel processing. Range(0, None) Use '0' to let IQ-TREE automatically determine the optimal number of cores to use. [default: 1]" name="pncores" optional="True" type="integer" min="0" value="1"/>
104 <param label="--p-n-runs: INTEGER Number of indepedent runs. Multiple independent Range(1, None) runs (e.g. 10) can outperform a single run in terms of likelihood maximisation. [default: 1]" name="pnruns" optional="True" type="integer" min="1" value="1"/>
105 <param label="--p-substitution-model: " name="psubstitutionmodel" optional="True" type="select">
106 <option selected="True" value="None">Selection is Optional</option>
107 <option value="JC">JC</option>
108 <option value="JC+I">JC+I</option>
109 <option value="JC+G">JC+G</option>
110 <option value="JC+I+G">JC+I+G</option>
111 <option value="JC+R2">JC+R2</option>
112 <option value="JC+R3">JC+R3</option>
113 <option value="JC+R4">JC+R4</option>
114 <option value="JC+R5">JC+R5</option>
115 <option value="JC+R6">JC+R6</option>
116 <option value="JC+R7">JC+R7</option>
117 <option value="JC+R8">JC+R8</option>
118 <option value="JC+R9">JC+R9</option>
119 <option value="JC+R10">JC+R10</option>
120 <option value="F81">F81</option>
121 <option value="F81+I">F81+I</option>
122 <option value="F81+G">F81+G</option>
123 <option value="F81+I+G">F81+I+G</option>
124 <option value="F81+R2">F81+R2</option>
125 <option value="F81+R3">F81+R3</option>
126 <option value="F81+R4">F81+R4</option>
127 <option value="F81+R5">F81+R5</option>
128 <option value="F81+R6">F81+R6</option>
129 <option value="F81+R7">F81+R7</option>
130 <option value="F81+R8">F81+R8</option>
131 <option value="F81+R9">F81+R9</option>
132 <option value="F81+R10">F81+R10</option>
133 <option value="K80">K80</option>
134 <option value="K80+I">K80+I</option>
135 <option value="K80+G">K80+G</option>
136 <option value="K80+I+G">K80+I+G</option>
137 <option value="K80+R2">K80+R2</option>
138 <option value="K80+R3">K80+R3</option>
139 <option value="K80+R4">K80+R4</option>
140 <option value="K80+R5">K80+R5</option>
141 <option value="K80+R6">K80+R6</option>
142 <option value="K80+R7">K80+R7</option>
143 <option value="K80+R8">K80+R8</option>
144 <option value="K80+R9">K80+R9</option>
145 <option value="K80+R10">K80+R10</option>
146 <option value="HKY">HKY</option>
147 <option value="HKY+I">HKY+I</option>
148 <option value="HKY+G">HKY+G</option>
149 <option value="HKY+I+G">HKY+I+G</option>
150 <option value="HKY+R2">HKY+R2</option>
151 <option value="HKY+R3">HKY+R3</option>
152 <option value="HKY+R4">HKY+R4</option>
153 <option value="HKY+R5">HKY+R5</option>
154 <option value="HKY+R6">HKY+R6</option>
155 <option value="HKY+R7">HKY+R7</option>
156 <option value="HKY+R8">HKY+R8</option>
157 <option value="HKY+R9">HKY+R9</option>
158 <option value="HKY+R10">HKY+R10</option>
159 <option value="TNe">TNe</option>
160 <option value="TNe+I">TNe+I</option>
161 <option value="TNe+G">TNe+G</option>
162 <option value="TNe+I+G">TNe+I+G</option>
163 <option value="TNe+R2">TNe+R2</option>
164 <option value="TNe+R3">TNe+R3</option>
165 <option value="TNe+R4">TNe+R4</option>
166 <option value="TNe+R5">TNe+R5</option>
167 <option value="TNe+R6">TNe+R6</option>
168 <option value="TNe+R7">TNe+R7</option>
169 <option value="TNe+R8">TNe+R8</option>
170 <option value="TNe+R9">TNe+R9</option>
171 <option value="TNe+R10">TNe+R10</option>
172 <option value="TN">TN</option>
173 <option value="TN+I">TN+I</option>
174 <option value="TN+G">TN+G</option>
175 <option value="TN+I+G">TN+I+G</option>
176 <option value="TN+R2">TN+R2</option>
177 <option value="TN+R3">TN+R3</option>
178 <option value="TN+R4">TN+R4</option>
179 <option value="TN+R5">TN+R5</option>
180 <option value="TN+R6">TN+R6</option>
181 <option value="TN+R7">TN+R7</option>
182 <option value="TN+R8">TN+R8</option>
183 <option value="TN+R9">TN+R9</option>
184 <option value="TN+R10">TN+R10</option>
185 <option value="K81">K81</option>
186 <option value="K81+I">K81+I</option>
187 <option value="K81+G">K81+G</option>
188 <option value="K81+I+G">K81+I+G</option>
189 <option value="K81+R2">K81+R2</option>
190 <option value="K81+R3">K81+R3</option>
191 <option value="K81+R4">K81+R4</option>
192 <option value="K81+R5">K81+R5</option>
193 <option value="K81+R6">K81+R6</option>
194 <option value="K81+R7">K81+R7</option>
195 <option value="K81+R8">K81+R8</option>
196 <option value="K81+R9">K81+R9</option>
197 <option value="K81+R10">K81+R10</option>
198 <option value="K81u">K81u</option>
199 <option value="K81u+I">K81u+I</option>
200 <option value="K81u+G">K81u+G</option>
201 <option value="K81u+I+G">K81u+I+G</option>
202 <option value="K81u+R2">K81u+R2</option>
203 <option value="K81u+R3">K81u+R3</option>
204 <option value="K81u+R4">K81u+R4</option>
205 <option value="K81u+R5">K81u+R5</option>
206 <option value="K81u+R6">K81u+R6</option>
207 <option value="K81u+R7">K81u+R7</option>
208 <option value="K81u+R8">K81u+R8</option>
209 <option value="K81u+R9">K81u+R9</option>
210 <option value="K81u+R10">K81u+R10</option>
211 <option value="TPM2">TPM2</option>
212 <option value="TPM2+I">TPM2+I</option>
213 <option value="TPM2+G">TPM2+G</option>
214 <option value="TPM2+I+G">TPM2+I+G</option>
215 <option value="TPM2+R2">TPM2+R2</option>
216 <option value="TPM2+R3">TPM2+R3</option>
217 <option value="TPM2+R4">TPM2+R4</option>
218 <option value="TPM2+R5">TPM2+R5</option>
219 <option value="TPM2+R6">TPM2+R6</option>
220 <option value="TPM2+R7">TPM2+R7</option>
221 <option value="TPM2+R8">TPM2+R8</option>
222 <option value="TPM2+R9">TPM2+R9</option>
223 <option value="TPM2+R10">TPM2+R10</option>
224 <option value="TPM2u">TPM2u</option>
225 <option value="TPM2u+I">TPM2u+I</option>
226 <option value="TPM2u+G">TPM2u+G</option>
227 <option value="TPM2u+I+G">TPM2u+I+G</option>
228 <option value="TPM2u+R2">TPM2u+R2</option>
229 <option value="TPM2u+R3">TPM2u+R3</option>
230 <option value="TPM2u+R4">TPM2u+R4</option>
231 <option value="TPM2u+R5">TPM2u+R5</option>
232 <option value="TPM2u+R6">TPM2u+R6</option>
233 <option value="TPM2u+R7">TPM2u+R7</option>
234 <option value="TPM2u+R8">TPM2u+R8</option>
235 <option value="TPM2u+R9">TPM2u+R9</option>
236 <option value="TPM2u+R10">TPM2u+R10</option>
237 <option value="TPM3">TPM3</option>
238 <option value="TPM3+I">TPM3+I</option>
239 <option value="TPM3+G">TPM3+G</option>
240 <option value="TPM3+I+G">TPM3+I+G</option>
241 <option value="TPM3+R2">TPM3+R2</option>
242 <option value="TPM3+R3">TPM3+R3</option>
243 <option value="TPM3+R4">TPM3+R4</option>
244 <option value="TPM3+R5">TPM3+R5</option>
245 <option value="TPM3+R6">TPM3+R6</option>
246 <option value="TPM3+R7">TPM3+R7</option>
247 <option value="TPM3+R8">TPM3+R8</option>
248 <option value="TPM3+R9">TPM3+R9</option>
249 <option value="TPM3+R10">TPM3+R10</option>
250 <option value="TPM3u">TPM3u</option>
251 <option value="TPM3u+I">TPM3u+I</option>
252 <option value="TPM3u+G">TPM3u+G</option>
253 <option value="TPM3u+I+G">TPM3u+I+G</option>
254 <option value="TPM3u+R2">TPM3u+R2</option>
255 <option value="TPM3u+R3">TPM3u+R3</option>
256 <option value="TPM3u+R4">TPM3u+R4</option>
257 <option value="TPM3u+R5">TPM3u+R5</option>
258 <option value="TPM3u+R6">TPM3u+R6</option>
259 <option value="TPM3u+R7">TPM3u+R7</option>
260 <option value="TPM3u+R8">TPM3u+R8</option>
261 <option value="TPM3u+R9">TPM3u+R9</option>
262 <option value="TPM3u+R10">TPM3u+R10</option>
263 <option value="TIMe">TIMe</option>
264 <option value="TIMe+I">TIMe+I</option>
265 <option value="TIMe+G">TIMe+G</option>
266 <option value="TIMe+I+G">TIMe+I+G</option>
267 <option value="TIMe+R2">TIMe+R2</option>
268 <option value="TIMe+R3">TIMe+R3</option>
269 <option value="TIMe+R4">TIMe+R4</option>
270 <option value="TIMe+R5">TIMe+R5</option>
271 <option value="TIMe+R6">TIMe+R6</option>
272 <option value="TIMe+R7">TIMe+R7</option>
273 <option value="TIMe+R8">TIMe+R8</option>
274 <option value="TIMe+R9">TIMe+R9</option>
275 <option value="TIMe+R10">TIMe+R10</option>
276 <option value="TIM">TIM</option>
277 <option value="TIM+I">TIM+I</option>
278 <option value="TIM+G">TIM+G</option>
279 <option value="TIM+I+G">TIM+I+G</option>
280 <option value="TIM+R2">TIM+R2</option>
281 <option value="TIM+R3">TIM+R3</option>
282 <option value="TIM+R4">TIM+R4</option>
283 <option value="TIM+R5">TIM+R5</option>
284 <option value="TIM+R6">TIM+R6</option>
285 <option value="TIM+R7">TIM+R7</option>
286 <option value="TIM+R8">TIM+R8</option>
287 <option value="TIM+R9">TIM+R9</option>
288 <option value="TIM+R10">TIM+R10</option>
289 <option value="TIM2e">TIM2e</option>
290 <option value="TIM2e+I">TIM2e+I</option>
291 <option value="TIM2e+G">TIM2e+G</option>
292 <option value="TIM2e+I+G">TIM2e+I+G</option>
293 <option value="TIM2e+R2">TIM2e+R2</option>
294 <option value="TIM2e+R3">TIM2e+R3</option>
295 <option value="TIM2e+R4">TIM2e+R4</option>
296 <option value="TIM2e+R5">TIM2e+R5</option>
297 <option value="TIM2e+R6">TIM2e+R6</option>
298 <option value="TIM2e+R7">TIM2e+R7</option>
299 <option value="TIM2e+R8">TIM2e+R8</option>
300 <option value="TIM2e+R9">TIM2e+R9</option>
301 <option value="TIM2e+R10">TIM2e+R10</option>
302 <option value="TIM2">TIM2</option>
303 <option value="TIM2+I">TIM2+I</option>
304 <option value="TIM2+G">TIM2+G</option>
305 <option value="TIM2+I+G">TIM2+I+G</option>
306 <option value="TIM2+R2">TIM2+R2</option>
307 <option value="TIM2+R3">TIM2+R3</option>
308 <option value="TIM2+R4">TIM2+R4</option>
309 <option value="TIM2+R5">TIM2+R5</option>
310 <option value="TIM2+R6">TIM2+R6</option>
311 <option value="TIM2+R7">TIM2+R7</option>
312 <option value="TIM2+R8">TIM2+R8</option>
313 <option value="TIM2+R9">TIM2+R9</option>
314 <option value="TIM2+R10">TIM2+R10</option>
315 <option value="TIM3e">TIM3e</option>
316 <option value="TIM3e+I">TIM3e+I</option>
317 <option value="TIM3e+G">TIM3e+G</option>
318 <option value="TIM3e+I+G">TIM3e+I+G</option>
319 <option value="TIM3e+R2">TIM3e+R2</option>
320 <option value="TIM3e+R3">TIM3e+R3</option>
321 <option value="TIM3e+R4">TIM3e+R4</option>
322 <option value="TIM3e+R5">TIM3e+R5</option>
323 <option value="TIM3e+R6">TIM3e+R6</option>
324 <option value="TIM3e+R7">TIM3e+R7</option>
325 <option value="TIM3e+R8">TIM3e+R8</option>
326 <option value="TIM3e+R9">TIM3e+R9</option>
327 <option value="TIM3e+R10">TIM3e+R10</option>
328 <option value="TIM3">TIM3</option>
329 <option value="TIM3+I">TIM3+I</option>
330 <option value="TIM3+G">TIM3+G</option>
331 <option value="TIM3+I+G">TIM3+I+G</option>
332 <option value="TIM3+R2">TIM3+R2</option>
333 <option value="TIM3+R3">TIM3+R3</option>
334 <option value="TIM3+R4">TIM3+R4</option>
335 <option value="TIM3+R5">TIM3+R5</option>
336 <option value="TIM3+R6">TIM3+R6</option>
337 <option value="TIM3+R7">TIM3+R7</option>
338 <option value="TIM3+R8">TIM3+R8</option>
339 <option value="TIM3+R9">TIM3+R9</option>
340 <option value="TIM3+R10">TIM3+R10</option>
341 <option value="TVMe">TVMe</option>
342 <option value="TVMe+I">TVMe+I</option>
343 <option value="TVMe+G">TVMe+G</option>
344 <option value="TVMe+I+G">TVMe+I+G</option>
345 <option value="TVMe+R2">TVMe+R2</option>
346 <option value="TVMe+R3">TVMe+R3</option>
347 <option value="TVMe+R4">TVMe+R4</option>
348 <option value="TVMe+R5">TVMe+R5</option>
349 <option value="TVMe+R6">TVMe+R6</option>
350 <option value="TVMe+R7">TVMe+R7</option>
351 <option value="TVMe+R8">TVMe+R8</option>
352 <option value="TVMe+R9">TVMe+R9</option>
353 <option value="TVMe+R10">TVMe+R10</option>
354 <option value="TVM">TVM</option>
355 <option value="TVM+I">TVM+I</option>
356 <option value="TVM+G">TVM+G</option>
357 <option value="TVM+I+G">TVM+I+G</option>
358 <option value="TVM+R2">TVM+R2</option>
359 <option value="TVM+R3">TVM+R3</option>
360 <option value="TVM+R4">TVM+R4</option>
361 <option value="TVM+R5">TVM+R5</option>
362 <option value="TVM+R6">TVM+R6</option>
363 <option value="TVM+R7">TVM+R7</option>
364 <option value="TVM+R8">TVM+R8</option>
365 <option value="TVM+R9">TVM+R9</option>
366 <option value="TVM+R10">TVM+R10</option>
367 <option value="SYM">SYM</option>
368 <option value="SYM+I">SYM+I</option>
369 <option value="SYM+G">SYM+G</option>
370 <option value="SYM+I+G">SYM+I+G</option>
371 <option value="SYM+R2">SYM+R2</option>
372 <option value="SYM+R3">SYM+R3</option>
373 <option value="SYM+R4">SYM+R4</option>
374 <option value="SYM+R5">SYM+R5</option>
375 <option value="SYM+R6">SYM+R6</option>
376 <option value="SYM+R7">SYM+R7</option>
377 <option value="SYM+R8">SYM+R8</option>
378 <option value="SYM+R9">SYM+R9</option>
379 <option value="SYM+R10">SYM+R10</option>
380 <option value="GTR">GTR</option>
381 <option value="GTR+I">GTR+I</option>
382 <option value="GTR+G">GTR+G</option>
383 <option value="GTR+I+G">GTR+I+G</option>
384 <option value="GTR+R2">GTR+R2</option>
385 <option value="GTR+R3">GTR+R3</option>
386 <option value="GTR+R4">GTR+R4</option>
387 <option value="GTR+R5">GTR+R5</option>
388 <option value="GTR+R6">GTR+R6</option>
389 <option value="GTR+R7">GTR+R7</option>
390 <option value="GTR+R8">GTR+R8</option>
391 <option value="GTR+R9">GTR+R9</option>
392 <option value="GTR+R10">GTR+R10</option>
393 <option value="MFP">MFP</option>
394 <option value="TEST">TEST</option>
395 </param>
396 <param label="--p-bootstrap-replicates: INTEGER Range(1000, None) The number of bootstrap searches to perform. Minimum of 1000 recomended. [default: 1000]" name="pbootstrapreplicates" optional="True" type="integer" min="1000" value="1000"/>
397 <param label="--p-n-init-pars-trees: INTEGER Range(1, None) Number of initial parsimony trees. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pninitparstrees" optional="True" type="integer" min="1"/>
398 <param label="--p-n-top-init-trees: INTEGER Range(1, None) Number of top initial trees. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pntopinittrees" optional="True" type="integer" min="1"/>
399 <param label="--p-n-best-retain-trees: INTEGER Range(1, None) Number of best trees retained during search. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pnbestretaintrees" optional="True" type="integer" min="1"/>
400 <param label="--p-stop-iter: INTEGER Number of unsuccessful iterations to stop. If not Range(1, None) set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pstopiter" optional="True" type="integer" min="1"/>
401 <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"/>
402 <param label="--p-spr-radius: INTEGER Radius for parsimony SPR search. If not set, Range(1, None) program defaults will be used. See IQ-TREE manual for details. [optional]" name="psprradius" optional="True" type="integer" min="1"/>
403 <param label="--p-n-max-ufboot-iter: INTEGER Range(1, None) Maximum number of iterations. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pnmaxufbootiter" optional="True" type="integer" min="1"/>
404 <param label="--p-n-ufboot-steps: INTEGER Range(1, None) Number of iterations for UFBoot stopping rule. If not set, program defaults will be used.See IQ-TREE manual for details. [optional]" name="pnufbootsteps" optional="True" type="integer" min="1"/>
405 <param label="--p-min-cor-ufboot: NUMBER Range(0.51, 0.99) Minimum correlation coefficient. If not set, program defaults will be used.See IQ-TREE manual for details. [optional]" name="pmincorufboot" optional="True" type="float" min="0.51" max="0.99"/>
406 <param label="--p-ep-break-ufboot: NUMBER Range(0.01, 0.99) Epsilon value to break tie. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pepbreakufboot" optional="True" type="float" min="0.01" max="0.99"/>
407 <param label="--p-allnni: --p-no-allnni Perform more thorough NNI search. [default: False]" name="pallnni" selected="False" type="boolean"/>
408 <param label="--p-alrt: INTEGER Single branch test method. Number of bootstrap Range(1000, None) replicates to perform an SH-like approximate likelihood ratio test (SH-aLRT). Minimum of 1000 replicates is recomended. Set to '0' for parametric aLRT test. Can be used with other 'single branch test methods'. Values reported in the order of: alrt, lbp, abayes, ufboot. [optional]" name="palrt" optional="True" type="integer" min="1000"/>
409 <param label="--p-abayes: --p-no-abayes Single branch test method. Performs an approximate Bayes test. Can be used with other 'single branch test methods' and ultrafast bootstrap. Values reported in the order of: alrt, lbp, abayes, ufboot. [default: False]" name="pabayes" selected="False" type="boolean"/>
410 <param label="--p-lbp: INTEGER Single branch test method. Number of bootstrap Range(1000, None) replicates to perform a fast local bootstrap probability method. Minimum of 1000 replicates is recomended. Can be used with other 'single branch test methods'. Values reported in the order of: alrt, lbp, abayes, ufboot. [optional]" name="plbp" optional="True" type="integer" min="1000"/>
411 <param label="--p-bnni: --p-no-bnni Optimize UFBoot trees by NNI on bootstrap alignment. This option reduces the risk of overestimating branch supports with UFBoot due to severe model violations. [default: False]" name="pbnni" selected="False" type="boolean"/>
412 <param label="--p-safe: --p-no-safe Safe likelihood kernel to avoid numerical underflow. [default: False]" name="psafe" selected="False" type="boolean"/>
413 </inputs>
414 <outputs>
415 <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree"/>
416 </outputs>
417 <help><![CDATA[
418 Construct a phylogenetic tree with IQ-TREE with bootstrap supports.
419 ###################################################################
420
421 Construct a phylogenetic tree using IQ-TREE (http://www.iqtree.org/) with
422 automatic model selection and bootstrap supports.
423
424 Parameters
425 ----------
426 alignment : FeatureData[AlignedSequence]
427 Aligned sequences to be used for phylogenetic reconstruction.
428 seed : Int, optional
429 Random number seed. If not set, program defaults will be used. See IQ-
430 TREE manual for details.
431 n_runs : Int % Range(1, None), optional
432 Number of indepedent runs. Multiple independent runs (e.g. 10) can
433 outperform a single run in terms of likelihood maximisation.
434 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
435 Model of Nucleotide Substitution.If not provided, IQ-TREE will
436 determine the best fit substitution model automatically.
437 bootstrap_replicates : Int % Range(1000, None), optional
438 The number of bootstrap searches to perform. Minimum of 1000
439 recomended.
440 n_init_pars_trees : Int % Range(1, None), optional
441 Number of initial parsimony trees. If not set, program defaults will be
442 used. See IQ-TREE manual for details.
443 n_top_init_trees : Int % Range(1, None), optional
444 Number of top initial trees. If not set, program defaults will be used.
445 See IQ-TREE manual for details.
446 n_best_retain_trees : Int % Range(1, None), optional
447 Number of best trees retained during search. If not set, program
448 defaults will be used. See IQ-TREE manual for details.
449 stop_iter : Int % Range(1, None), optional
450 Number of unsuccessful iterations to stop. If not set, program defaults
451 will be used. See IQ-TREE manual for details.
452 perturb_nni_strength : Float % Range(0.01, 99), optional
453 Perturbation strength for randomized NNI. If not set, program defaults
454 will be used. See IQ-TREE manual for details.
455 spr_radius : Int % Range(1, None), optional
456 Radius for parsimony SPR search. If not set, program defaults will be
457 used. See IQ-TREE manual for details.
458 n_max_ufboot_iter : Int % Range(1, None), optional
459 Maximum number of iterations. If not set, program defaults will be
460 used. See IQ-TREE manual for details.
461 n_ufboot_steps : Int % Range(1, None), optional
462 Number of iterations for UFBoot stopping rule. If not set, program
463 defaults will be used.See IQ-TREE manual for details.
464 min_cor_ufboot : Float % Range(0.51, 0.99), optional
465 Minimum correlation coefficient. If not set, program defaults will be
466 used.See IQ-TREE manual for details.
467 ep_break_ufboot : Float % Range(0.01, 0.99), optional
468 Epsilon value to break tie. If not set, program defaults will be used.
469 See IQ-TREE manual for details.
470 allnni : Bool, optional
471 Perform more thorough NNI search.
472 alrt : Int % Range(1000, None), optional
473 Single branch test method. Number of bootstrap replicates to perform an
474 SH-like approximate likelihood ratio test (SH-aLRT). Minimum of 1000
475 replicates is recomended. Set to '0' for parametric aLRT test. Can be
476 used with other 'single branch test methods'. Values reported in the
477 order of: alrt, lbp, abayes, ufboot.
478 abayes : Bool, optional
479 Single branch test method. Performs an approximate Bayes test. Can be
480 used with other 'single branch test methods' and ultrafast bootstrap.
481 Values reported in the order of: alrt, lbp, abayes, ufboot.
482 lbp : Int % Range(1000, None), optional
483 Single branch test method. Number of bootstrap replicates to perform a
484 fast local bootstrap probability method. Minimum of 1000 replicates is
485 recomended. Can be used with other 'single branch test methods'. Values
486 reported in the order of: alrt, lbp, abayes, ufboot.
487 bnni : Bool, optional
488 Optimize UFBoot trees by NNI on bootstrap alignment. This option
489 reduces the risk of overestimating branch supports with UFBoot due to
490 severe model violations.
491 safe : Bool, optional
492 Safe likelihood kernel to avoid numerical underflow.
493
494 Returns
495 -------
496 tree : Phylogeny[Unrooted]
497 The resulting phylogenetic tree.
498 ]]></help>
499 <macros>
500 <import>qiime_citation.xml</import>
501 </macros>
502 <expand macro="qiime_citation"/>
503 </tool>